Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2112
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: 107201
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Found at i:4257 original size:12 final size:12
Alignment explanation
Indices: 4235--4263 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4225 TTTTAGATAG
4235 TATAT-AAATTT
1 TATATAAAATTT
4246 TATATAAAATTT
1 TATATAAAATTT
4258 TATATA
1 TATATA
4264 TATTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATAAAATTT
Found at i:4274 original size:12 final size:11
Alignment explanation
Indices: 4235--4270 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
4225 TTTTAGATAG
4235 TATATAAATTT
1 TATATAAATTT
4246 TATATAAAATTT
1 TATAT-AAATTT
*
4258 TATATATATTT
1 TATATAAATTT
4269 TA
1 TA
4271 ATATGTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATAAATTT
Found at i:4298 original size:11 final size:11
Alignment explanation
Indices: 4282--4316 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
4272 TATGTTTGTG
4282 TATTTTTATTA
1 TATTTTTATTA
4293 TATTTTTATTA
1 TATTTTTATTA
4304 T-TTTTTATTA
1 TATTTTTATTA
4314 TAT
1 TAT
4317 GTAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:4516 original size:20 final size:18
Alignment explanation
Indices: 4461--4532 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
4451 TTTTTGTGTT
4461 TAAATATTATA-AATTTATA
1 TAAA-ATTATATAATTTA-A
*
4480 TAAAATTTTAT-ATTTAA
1 TAAAATTATATAATTTAA
4497 TAATTAATTATATAATTTAA
1 TAA--AATTATATAATTTAA
* *
4517 TATATTTATAT-ATTTA
1 TAAAATTATATAATTTA
4533 TATTATATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 9 0.20
18 17 0.38
19 11 0.24
20 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAAATTATATAATTTAA
Found at i:4527 original size:8 final size:8
Alignment explanation
Indices: 4504--4579 Score: 50
Period size: 8 Copynumber: 9.1 Consensus size: 8
4494 TAATAATTAA
4504 TTATATAAT
1 TTATAT-AT
4513 TTAATATAT
1 TT-ATATAT
4522 TTATATAT
1 TTATATAT
4530 TTATATTAT
1 TTATA-TAT
4539 ATTAATATTAT
1 -TT-ATA-TAT
*
4550 TTTTATA-
1 TTATATAT
4557 TTATAT-T
1 TTATATAT
*
4564 TTA-ATGT
1 TTATATAT
*
4571 TTTTATAT
1 TTATATAT
4579 T
1 T
4580 ATTTTATACC
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
6 2 0.04
7 11 0.20
8 17 0.30
9 11 0.20
10 8 0.14
11 7 0.12
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (8 bp):
TTATATAT
Found at i:4541 original size:11 final size:11
Alignment explanation
Indices: 4525--4587 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
4515 AATATATTTA
4525 TATATTTATAT
1 TATATTTATAT
*
4536 TATATTAATAT
1 TATATTTATAT
*
4547 TATTTTTATAT
1 TATATTTATAT
*
4558 TATATTT-TAA
1 TATATTTATAT
* *
4568 TGTTTTTATAT
1 TATATTTATAT
4579 TAT-TTTATA
1 TATATTTATA
4588 CCGCACACCA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
10 13 0.31
11 29 0.69
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TATATTTATAT
Found at i:4557 original size:22 final size:21
Alignment explanation
Indices: 4517--4587 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
4507 TATAATTTAA
*
4517 TATATT-T-ATATATTTATAT
1 TATATTATAATATTTTTATAT
*
4536 TATATTAATATTATTTTTATAT
1 TATATT-ATAATATTTTTATAT
* *
4558 TATATTTTAATGTTTTTATAT
1 TATATTATAATATTTTTATAT
*
4579 TATTTTATA
1 TATATTATA
4588 CCGCACACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 6 0.14
21 20 0.48
22 16 0.38
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (21 bp):
TATATTATAATATTTTTATAT
Found at i:5611 original size:14 final size:14
Alignment explanation
Indices: 5589--5631 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5579 ATTAAAAATA
*
5589 ATTTTTATTTTAAT
1 ATTTATATTTTAAT
5603 ATTTATATTTT-AT
1 ATTTATATTTTAAT
* *
5616 AATTATATTTAAAT
1 ATTTATATTTTAAT
5630 AT
1 AT
5632 AAATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTATATTTTAAT
Found at i:5663 original size:18 final size:17
Alignment explanation
Indices: 5616--5663 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
5606 TATATTTTAT
* *
5616 AATTATATTTAAATATA
1 AATTATATTTTAATAAA
5633 AATATATTATTTTAATAAA
1 AAT-TA-TATTTTAATAAA
5652 AATTACTATTTT
1 AATTA-TATTTT
5664 TCGACTTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 10 0.38
19 13 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTATATTTTAATAAA
Found at i:6029 original size:6 final size:6
Alignment explanation
Indices: 6018--6055 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
6008 TATAAAAAAC
6018 AATATA AATATA AATAT- AATATA AA-AT- AATATA AATAT
1 AATATA AATATA AATATA AATATA AATATA AATATA AATAT
6056 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 2 0.07
5 9 0.31
6 18 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:6048 original size:10 final size:11
Alignment explanation
Indices: 6018--6055 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
6008 TATAAAAAAC
6018 AATATAAATATA
1 AATAT-AATATA
6030 AATATAATATA
1 AATATAATATA
6041 AA-ATAATATA
1 AATATAATATA
6051 AATAT
1 AATAT
6056 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.40
11 10 0.40
12 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATATAATATA
Found at i:6073 original size:27 final size:26
Alignment explanation
Indices: 6043--6106 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
6033 ATAATATAAA
* *
6043 ATAATATAAATATTTTAAAATTTTTAT
1 ATAATATAAATATATT-AAATTTTAAT
*
6070 ATAATATTAAT-TATTAAATTTTAAT
1 ATAATATAAATATATTAAATTTTAAT
6095 AT-AT-TAAATATA
1 ATAATATAAATATA
6107 ATTATAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 4 0.12
24 4 0.12
25 11 0.34
26 3 0.09
27 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATAATATAAATATATTAAATTTTAAT
Found at i:6619 original size:8 final size:8
Alignment explanation
Indices: 6608--6632 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6598 AATATAAAAA
6608 TATTATTT
1 TATTATTT
6616 TATTATTT
1 TATTATTT
6624 TATTATTT
1 TATTATTT
6632 T
1 T
6633 TGCTACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:7512 original size:33 final size:34
Alignment explanation
Indices: 7448--7516 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
7438 AAAAAAATTA
* *
7448 AAAAAATTAATTTAATATATATGTTTTATTTTTT
1 AAAAAATTAATTTAATATATATATTTAATTTTTT
*
7482 AAAAAATTAA-TTAGATTTA-ATATTTAATTTTTT
1 AAAAAATTAATTTA-ATATATATATTTAATTTTTT
7515 AA
1 AA
7517 TTTTATGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (34 bp):
AAAAAATTAATTTAATATATATATTTAATTTTTT
Found at i:7755 original size:20 final size:19
Alignment explanation
Indices: 7709--7758 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
7699 TTATTTAATA
7709 TTTATTT-AATATTAAAAT
1 TTTATTTAAATATTAAAAT
* *
7727 TATATTTTAAATATTTACAAT
1 TTTA-TTTAAATA-TTAAAAT
7748 TTTATTTAAAT
1 TTTATTTAAAT
7759 TAAATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 11 0.42
21 9 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATTTAAATATTAAAAT
Found at i:8137 original size:2 final size:2
Alignment explanation
Indices: 8130--8169 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8120 TCATTTATGT
8130 TA TA 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
8170 ATGGAAGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21038 original size:21 final size:21
Alignment explanation
Indices: 21012--21052 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21002 TGTACATTTG
*
21012 AATGAAATGATGCACTTATTA
1 AATGAAATAATGCACTTATTA
* *
21033 AATGAATTAATGCATTTATT
1 AATGAAATAATGCACTTATT
21053 GGATGAAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (21 bp):
AATGAAATAATGCACTTATTA
Found at i:21620 original size:11 final size:11
Alignment explanation
Indices: 21593--21626 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
21583 ATATCTATAT
21593 CTAATATTCACAC
1 CTAA-ATTCA-AC
21606 CTAAATTCAAC
1 CTAAATTCAAC
21617 CTAAATTCAA
1 CTAAATTCAA
21627 GTAACATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 5 0.24
13 4 0.19
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (11 bp):
CTAAATTCAAC
Found at i:25563 original size:21 final size:21
Alignment explanation
Indices: 25491--25564 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
25481 TTTTTTTAAA
*
25491 ATTTATATTATATAAATTAAAAT
1 ATTTA-ATT-TATAAATTATAAT
*
25514 -TTTAATTTAATTAATTTATAA-
1 ATTTAATTT-A-TAAATTATAAT
*
25535 AATT-ATTTATAAATTATAAT
1 ATTTAATTTATAAATTATAAT
25555 ATTTAATTTA
1 ATTTAATTTA
25565 CTTGATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
19 9 0.22
20 5 0.12
21 13 0.32
22 14 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATTTATAAATTATAAT
Found at i:25951 original size:2 final size:2
Alignment explanation
Indices: 25944--25975 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25934 TGTTTATTTG
25944 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
25976 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26029 original size:2 final size:2
Alignment explanation
Indices: 26024--26048 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26014 ATATATATAT
26024 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 A
26049 AGAACTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26770 original size:2 final size:2
Alignment explanation
Indices: 26763--26787 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26753 ACGTTTTAAC
26763 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
26788 GTGGACCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27854 original size:18 final size:17
Alignment explanation
Indices: 27831--27866 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
27821 CTGCATCCAG
27831 ATCGACATATCATGAGAA
1 ATCGACATATCAT-AGAA
*
27849 ATCGACGTATCATAGAA
1 ATCGACATATCATAGAA
27866 A
1 A
27867 GCATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (17 bp):
ATCGACATATCATAGAA
Found at i:30644 original size:4 final size:4
Alignment explanation
Indices: 30635--30665 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
30625 CTAAACATAA
*
30635 AAAT AAAT AAAT AAAT AAAT AAAC AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
30666 AAGATACTGA
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:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:31787 original size:15 final size:16
Alignment explanation
Indices: 31765--31805 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
31755 TTTAAGTTTG
*
31765 AATTATTTTTATT-TA
1 AATTATTTTAATTATA
*
31780 AGTTATTTTAATTATA
1 AATTATTTTAATTATA
31796 AATTATTTTA
1 AATTATTTTA
31806 GTTTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
AATTATTTTAATTATA
Found at i:31813 original size:22 final size:22
Alignment explanation
Indices: 31785--31826 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31775 ATTTAAGTTA
31785 TTTTAATTATAAATTATTTTAG
1 TTTTAATTATAAATTATTTTAG
* *
31807 TTTTAATTTTACATTATTTT
1 TTTTAATTATAAATTATTTT
31827 GAATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTAATTATAAATTATTTTAG
Found at i:31833 original size:22 final size:22
Alignment explanation
Indices: 31786--31839 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
31776 TTTAAGTTAT
*
31786 TTTAATTATAAATTATTTTAGT
1 TTTAATTATAAATTATTTTAGA
* *
31808 TTTAATTTTACATTATTTT-GAA
1 TTTAATTATAAATTATTTTAG-A
31830 TTTAAATTAT
1 TTT-AATTAT
31840 TTAGGTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 20 0.77
23 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTAATTATAAATTATTTTAGA
Found at i:31950 original size:37 final size:38
Alignment explanation
Indices: 31904--31977 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 38
31894 TTATTTTGAA
* * *
31904 TTCAGATTAATCAGGTTTAA-TACTTGAGTTAATCAAG
1 TTCAAATTAATCAAGTTTAACTACTAGAGTTAATCAAG
* *
31941 TTCAAATTAATGAAGTTTAACTACTAGAGTTTATCAA
1 TTCAAATTAATCAAGTTTAACTACTAGAGTTAATCAA
31978 ATTTGATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (38 bp):
TTCAAATTAATCAAGTTTAACTACTAGAGTTAATCAAG
Found at i:32013 original size:16 final size:16
Alignment explanation
Indices: 31994--32029 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31984 TTATTTTGAG
31994 TTTAAGTCATTTCAAA
1 TTTAAGTCATTTCAAA
* *
32010 TTTAATTCATTTCAAG
1 TTTAAGTCATTTCAAA
32026 TTTA
1 TTTA
32030 GTTAGTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTAAGTCATTTCAAA
Found at i:32097 original size:17 final size:17
Alignment explanation
Indices: 32039--32102 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 17
32029 AGTTAGTTCA
*
32039 TTTCAAGTTCAGATTAT
1 TTTCAAGTTTAGATTAT
* * *
32056 TCTGAA-TTTA-AGTAAT
1 TTTCAAGTTTAGA-TTAT
32072 TTT-AAGTTTAGATTAT
1 TTTCAAGTTTAGATTAT
32088 TTTCAAGTTTAGATT
1 TTTCAAGTTTAGATT
32103 GATATGGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
15 3 0.08
16 18 0.49
17 16 0.43
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (17 bp):
TTTCAAGTTTAGATTAT
Found at i:33025 original size:24 final size:25
Alignment explanation
Indices: 32994--33054 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 25
32984 CTCATAATTA
32994 ATAA-AAATTTAAAAAA-TACTTTT
1 ATAATAAATTTAAAAAATTACTTTT
*
33017 ATAATAAA-TTAAAAAATTATTTTT
1 ATAATAAATTTAAAAAATTACTTTT
33041 ATAATAAATTTAAA
1 ATAATAAATTTAAA
33055 TAAAAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 12 0.35
24 17 0.50
25 5 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATAAATTTAAAAAATTACTTTT
Found at i:35897 original size:165 final size:169
Alignment explanation
Indices: 35726--36124 Score: 391
Period size: 165 Copynumber: 2.3 Consensus size: 169
35716 ATTTCATATG
*
35726 ATAAAATTTGAATTTTAAATTTATTAAATATCAATTTTTATTAAAAATTAATGAATCGATCAAAT
1 ATAAAATTTGAATTTTAAATTTATTAAATATCAATTTTTA-TAAAAACTAATGAATCGATCAAAT
* * *
35791 TAAATTTTAGATTCTATAAGATAAAATTTTAATCTCGAACCTTCT-AATTGCCATTTTT-T-AAA
65 TAAATTTTAGATTCTATAAGATAAAATTTAAATCTCAAACCTGCTAAATT-CCATTTTTGTAAAA
* * *
35853 GGTGACT-AATGAATTAACTG-AATTT-CAA-ATTCTACATA
129 AGTGA-TAAATAAATTAACTGAAATTTAAAATATTCTACATA
* * * ** * ** * ** *
35891 ATAAAATTTGAATATCAAATGTGCTAAATATC-ATCTATTATAAGTGACTAATAAATTAATTAAA
1 ATAAAATTTGAATTTTAAATTTATTAAATATCAAT-TTTTATAA-AAACTAATGAATCGATCAAA
* * * **
35955 TTAAATTTTAGATTTTATAAGATAAAATTTAAATTTTAAACCTGCTAAATTTTATTTTTGTAAAA
64 TTAAATTTTAGATTCTATAAGATAAAATTTAAATCTCAAACCTGCTAAATTCCATTTTTGTAAAA
* *
36020 AGTGATAAATAAATTAACTGAACTAAATTTAAAATATTTTATATA
129 AGTGATAAATAAATTAACTG----AAATTTAAAATATTCTACATA
* * *
36065 ATAAAATTTAAATTTTAAATTTATTAAATATCATTTTTTATAAATAACTAATGAACCGAT
1 ATAAAATTTGAATTTTAAATTTATTAAATATCAATTTTTATAAA-AACTAATGAATCGAT
36125 TTAACTAAAT
Statistics
Matches: 179, Mismatches: 40, Indels: 21
0.75 0.17 0.09
Matches are distributed among these distances:
164 5 0.03
165 90 0.50
166 6 0.03
167 19 0.11
172 5 0.03
173 2 0.01
174 51 0.28
175 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.41
Consensus pattern (169 bp):
ATAAAATTTGAATTTTAAATTTATTAAATATCAATTTTTATAAAAACTAATGAATCGATCAAATT
AAATTTTAGATTCTATAAGATAAAATTTAAATCTCAAACCTGCTAAATTCCATTTTTGTAAAAAG
TGATAAATAAATTAACTGAAATTTAAAATATTCTACATA
Found at i:36512 original size:23 final size:23
Alignment explanation
Indices: 36445--36516 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
36435 TATTTAAATA
*
36445 ATATTAAAATATTAAAATTATTTTT
1 ATATT-AAATATTAAAATT-TTTAT
*
36470 ATATT-AATATTTATATATTTTTAT
1 ATATTAAATA-TTA-AAATTTTTAT
36494 A-ATTAAATTATTAAAATTTTTAT
1 ATATTAAA-TATTAAAATTTTTAT
36517 TTAAAATCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 16 0.40
24 13 0.32
25 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTAAATATTAAAATTTTTAT
Found at i:37220 original size:15 final size:15
Alignment explanation
Indices: 37202--37231 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37192 ATTTAAATAT
*
37202 AATTTTTTTAATTTA
1 AATTTATTTAATTTA
37217 AATTTATTTAATTTA
1 AATTTATTTAATTTA
37232 TTGGTAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTATTTAATTTA
Found at i:37748 original size:16 final size:16
Alignment explanation
Indices: 37725--37774 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
37715 TTATTGATGG
37725 TTAAATTTACGAATAA
1 TTAAATTTACGAATAA
* ** * *
37741 TTAGATTTAATATTTA
1 TTAAATTTACGAATAA
37757 TTAAATTTACGAATAA
1 TTAAATTTACGAATAA
37773 TT
1 TT
37775 TTATTTAATA
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (16 bp):
TTAAATTTACGAATAA
Found at i:37797 original size:32 final size:31
Alignment explanation
Indices: 37727--37827 Score: 116
Period size: 32 Copynumber: 3.2 Consensus size: 31
37717 ATTGATGGTT
* *
37727 AAATTTACGAATAATTAGATTTAATATTTATT
1 AAATTTACGAATAATTATATTTAATA-TTATC
*
37759 AAATTTACGAATAATTTTATTTAATATTCATC
1 AAATTTACGAATAATTATATTTAATATT-ATC
* *
37791 ACATTTAC-AAGTAATTATATCTAAT-TTATC
1 AAATTTACGAA-TAATTATATTTAATATTATC
37821 AAATTTA
1 AAATTTA
37828 TTATTAATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 9 0.15
31 6 0.10
32 45 0.75
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (31 bp):
AAATTTACGAATAATTATATTTAATATTATC
Found at i:39581 original size:2 final size:2
Alignment explanation
Indices: 39574--39615 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
39564 TAAACTAAGA
39574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39615 A
1 A
39616 ACAATTCATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39664 original size:21 final size:21
Alignment explanation
Indices: 39615--39656 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
39605 TATATAATAT
39615 AACAATTCATATTTTCAGAAG
1 AACAATTCATATTTTCAGAAG
39636 AACAATTCATATTTTCAGAAG
1 AACAATTCATATTTTCAGAAG
39657 CCGAATTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (21 bp):
AACAATTCATATTTTCAGAAG
Found at i:42277 original size:2 final size:2
Alignment explanation
Indices: 42270--42317 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
42260 TGAAAATTTT
42270 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
42312 AG AG AG
1 AG AG AG
42318 CTGCTAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45180 original size:23 final size:23
Alignment explanation
Indices: 45130--45181 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
45120 AAATTATTTT
** * *
45130 ATATTTATATATTTTTTAAGAAT
1 ATATTTATATAAATTTTAAAAAA
*
45153 TTATTTATATAAATTTTAAAAAA
1 ATATTTATATAAATTTTAAAAAA
45176 ATATTT
1 ATATTT
45182 TTATTTATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATATTTATATAAATTTTAAAAAA
Found at i:45273 original size:23 final size:23
Alignment explanation
Indices: 45228--45278 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
45218 TTTTATATAA
45228 TTAAA-TTTAAAATTATTAGA-T
1 TTAAATTTTAAAATTATTAGATT
*
45249 TTAAATTTTAAAATTTTTTAGATT
1 TTAAATTTTAAAA-TTATTAGATT
45273 TTAAAT
1 TTAAAT
45279 AAAATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 5 0.19
22 7 0.27
23 7 0.27
24 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TTAAATTTTAAAATTATTAGATT
Found at i:45303 original size:18 final size:17
Alignment explanation
Indices: 45273--45316 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
45263 TTTTTAGATT
45273 TTAAATAAAATATTAAAA
1 TTAAA-AAAATATTAAAA
*
45291 TTAAAAAATATATTTAAA
1 TTAAAAAA-ATATTAAAA
45309 TATAAAAA
1 T-TAAAAA
45317 TAAGATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAAAAATATTAAAA
Found at i:45511 original size:13 final size:13
Alignment explanation
Indices: 45493--45521 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
45483 TAAATTATTA
45493 AAAAATATATTTT
1 AAAAATATATTTT
45506 AAAAATATATTTT
1 AAAAATATATTTT
45519 AAA
1 AAA
45522 CAGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAAATATATTTT
Found at i:45712 original size:23 final size:23
Alignment explanation
Indices: 45686--45730 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
45676 AGATATTTGT
45686 AATTTATT-AAATATCTAAATTTA
1 AATTTATTCAAA-ATCTAAATTTA
*
45709 AATTTATTCAAAATTTAAATTT
1 AATTTATTCAAAATCTAAATTT
45731 TTTATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTTATTCAAAATCTAAATTTA
Found at i:47665 original size:2 final size:2
Alignment explanation
Indices: 47658--47687 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47648 AGACAAAGGA
47658 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
47688 TTATTATAGA
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:48953 original size:12 final size:12
Alignment explanation
Indices: 48936--48961 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48926 GTGGCAAACA
48936 AATGGGGGTAGT
1 AATGGGGGTAGT
48948 AATGGGGGTAGT
1 AATGGGGGTAGT
48960 AA
1 AA
48962 CTAGGTTAGT
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:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (12 bp):
AATGGGGGTAGT
Found at i:53677 original size:22 final size:21
Alignment explanation
Indices: 53647--53704 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
53637 AAATTAAAAT
* *
53647 ATTTTTTAATAATTAAATTTAA
1 ATTTATTAAT-ATTAAATATAA
*
53669 ATTTATTAATTTTAAATATAA
1 ATTTATTAATATTAAATATAA
*
53690 ATATTATAAAT-TTAA
1 AT-TTATTAATATTAA
53705 TTAATATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTATTAATATTAAATATAA
Found at i:53685 original size:21 final size:22
Alignment explanation
Indices: 53659--53702 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
53649 TTTTTAATAA
* *
53659 TTAAATTTAAAT-TTATTAATT
1 TTAAATATAAATATTATAAATT
53680 TTAAATATAAATATTATAAATT
1 TTAAATATAAATATTATAAATT
53702 T
1 T
53703 AATTAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATATAAATATTATAAATT
Found at i:54830 original size:23 final size:24
Alignment explanation
Indices: 54804--54856 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
54794 ATTTATATTA
*
54804 TTATAT-AAAATAATTTTAAAAAT
1 TTATATGAAAATAAGTTTAAAAAT
**
54827 TTATATGAATTTAAGTTTAAAAAT
1 TTATATGAAAATAAGTTTAAAAAT
54851 TTATAT
1 TTATAT
54857 TATCATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
TTATATGAAAATAAGTTTAAAAAT
Found at i:54843 original size:55 final size:55
Alignment explanation
Indices: 54771--54882 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
54761 TTTTAAATTT
*
54771 TTTATATGAATTTAAGTTTAAAAATTTATATTATTATATAAAATAATTTTAAAAA
1 TTTATATGAATTTAAGTTTAAAAATTTATATTATCATATAAAATAATTTTAAAAA
*
54826 TTTATATGAATTTAAGTTTAAAAATTTATATTATCATTTAAAATAATTTTAAAAA
1 TTTATATGAATTTAAGTTTAAAAATTTATATTATCATATAAAATAATTTTAAAAA
54881 TT
1 TT
54883 AATCTTTATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (55 bp):
TTTATATGAATTTAAGTTTAAAAATTTATATTATCATATAAAATAATTTTAAAAA
Found at i:58170 original size:12 final size:12
Alignment explanation
Indices: 58153--58195 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
58143 TAAGTATTTA
58153 TTTATTTATATT
1 TTTATTTATATT
58165 TTTATTTATA-T
1 TTTATTTATATT
58176 TTTATCTTA-ATT
1 TTTAT-TTATATT
58188 TTT-TTTAT
1 TTTATTTAT
58196 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 3 0.11
11 8 0.29
12 17 0.61
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTTATATT
Found at i:58188 original size:23 final size:22
Alignment explanation
Indices: 58153--58212 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
58143 TAAGTATTTA
58153 TTTATTTATATTTTTATTTATAT
1 TTTATTTATATTTTT-TTTATAT
*
58176 TTTATCTTA-ATTTTTTTTATTAA
1 TTTAT-TTATATTTTTTTTA-TAT
*
58199 TTT-TTTAAATTTTT
1 TTTATTTATATTTTT
58213 GTGATTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 3 0.09
22 11 0.33
23 16 0.48
24 3 0.09
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATTTATATTTTTTTTATAT
Found at i:58896 original size:3 final size:3
Alignment explanation
Indices: 58888--58927 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
58878 ATATTAGATT
58888 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
58928 AACATTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:59109 original size:23 final size:24
Alignment explanation
Indices: 59076--59121 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
59066 ATTATATATT
59076 AATTTTATTATTTATTAGTTTATG
1 AATTTTATTATTTATTAGTTTATG
* *
59100 AATTTT-TTATTTTTTATTTTAT
1 AATTTTATTATTTATTAGTTTAT
59122 TTTTTATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
AATTTTATTATTTATTAGTTTATG
Found at i:59110 original size:19 final size:20
Alignment explanation
Indices: 59086--59132 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
59076 AATTTTATTA
59086 TTTATTAGTTTA-TGAATTT
1 TTTATTAGTTTATTGAATTT
* **
59105 TTTATT-TTTTATTTTATTT
1 TTTATTAGTTTATTGAATTT
59124 TTTATTAGT
1 TTTATTAGT
59133 ATAGCTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 4 0.18
19 17 0.77
20 1 0.05
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (20 bp):
TTTATTAGTTTATTGAATTT
Found at i:59121 original size:12 final size:12
Alignment explanation
Indices: 59104--59129 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59094 TTTATGAATT
59104 TTTTATTTTTTA
1 TTTTATTTTTTA
59116 TTTTATTTTTTA
1 TTTTATTTTTTA
59128 TT
1 TT
59130 AGTATAGCTA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:60461 original size:11 final size:11
Alignment explanation
Indices: 60430--60522 Score: 59
Period size: 11 Copynumber: 8.5 Consensus size: 11
60420 ATATTTCGTG
*
60430 TATTTATATCA
1 TATTTATATTA
60441 TATTTATATTA
1 TATTTATATTA
* *
60452 TTTTTATATTG
1 TATTTATATTA
*
60463 TA-TAATATTTA
1 TATTTATA-TTA
*
60474 TAATTATA-T-
1 TATTTATATTA
*
60483 T-TTTATATTT
1 TATTTATATTA
*
60493 TATTTTTATTA
1 TATTTATATTA
*
60504 TATAATTATATGA
1 TAT--TTATATTA
60517 TATTTA
1 TATTTA
60523 AAATTATCGA
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
10 6 0.10
11 37 0.59
12 4 0.06
13 9 0.14
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTATATTA
Found at i:60513 original size:32 final size:30
Alignment explanation
Indices: 60450--60514 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
60440 ATATTTATAT
60450 TATTTTTATATTGTATAATATTTATAATTA
1 TATTTTTATATTGTATAATATTTATAATTA
* **
60480 TATTTTTATATTTTATTTTTATTATATAATTA
1 TATTTTTATATTGTA-TAATATT-TATAATTA
60512 TAT
1 TAT
60515 GATATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 14 0.47
31 5 0.17
32 11 0.37
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (30 bp):
TATTTTTATATTGTATAATATTTATAATTA
Found at i:60724 original size:11 final size:11
Alignment explanation
Indices: 60710--60738 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
60700 ATATAATATT
60710 ATATAAAAATA
1 ATATAAAAATA
60721 ATATAAAAATA
1 ATATAAAAATA
60732 ATATAAA
1 ATATAAA
60739 TATATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:60728 original size:10 final size:9
Alignment explanation
Indices: 60671--60775 Score: 63
Period size: 10 Copynumber: 11.0 Consensus size: 9
60661 CTTGAGATAT
*
60671 TATACAAAA
1 TATATAAAA
60680 TTATATAAAA
1 -TATATAAAA
*
60690 AATAATTAAAA
1 TAT-A-TAAAA
* *
60701 TATA-ATAT
1 TATATAAAA
60709 TATATAAAAA
1 TATAT-AAAA
60719 TAATATAAAA
1 T-ATATAAAA
60729 -ATAATATAAA
1 TAT-ATA-AAA
60739 TATAT-AAA
1 TATATAAAA
60747 TATATTAAAA
1 TATA-TAAAA
*
60757 TTTATATAAA
1 TATATA-AAA
60767 TATATAAAA
1 TATATAAAA
60776 AAATTAATGA
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
8 15 0.20
9 11 0.15
10 36 0.48
11 13 0.17
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (9 bp):
TATATAAAA
Found at i:60729 original size:38 final size:40
Alignment explanation
Indices: 60667--60774 Score: 122
Period size: 38 Copynumber: 2.9 Consensus size: 40
60657 GTAACTTGAG
*
60667 ATATTATA-CAAAATTATATAAAAAATAAT-TAAA-ATATA
1 ATATTATATAAAAATTATAT-AAAAATAATATAAATATATA
*
60705 ATATTATATAAAAATAATATAAAAATAATATAAATATATA
1 ATATTATATAAAAATTATATAAAAATAATATAAATATATA
* *
60745 A-A-TATATTAAAATT-TATATAAAT-ATATAAA
1 ATATTATATAAAAATTATATAAAAATAATATAAA
60775 AAAATTAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
36 7 0.11
37 8 0.13
38 27 0.44
39 14 0.23
40 6 0.10
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (40 bp):
ATATTATATAAAAATTATATAAAAATAATATAAATATATA
Found at i:60731 original size:8 final size:8
Alignment explanation
Indices: 60709--60774 Score: 57
Period size: 8 Copynumber: 8.0 Consensus size: 8
60699 AATATAATAT
60709 TATATAAA
1 TATATAAA
60717 -A-AT-AA
1 TATATAAA
*
60722 TATAAAAA
1 TATATAAA
60730 TAATATAAA
1 T-ATATAAA
60739 TATATAAA
1 TATATAAA
60747 TATATTAAAA
1 TATA-T-AAA
60757 TTTATATAAA
1 --TATATAAA
60767 TATATAAA
1 TATATAAA
60775 AAAATTAATG
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
5 2 0.04
6 3 0.06
7 2 0.04
8 22 0.46
9 8 0.17
10 6 0.12
11 1 0.02
12 4 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TATATAAA
Found at i:60745 original size:30 final size:29
Alignment explanation
Indices: 60681--60782 Score: 115
Period size: 28 Copynumber: 3.6 Consensus size: 29
60671 TATACAAAAT
60681 TATATAAAAAATAATTAAAATATAATAT---
1 TATAT-AAAAATAATTAAAA-ATAATATAAA
60709 TATATAAAAATAATATAAAAATAATATAAA
1 TATATAAAAATAAT-TAAAAATAATATAAA
* * *
60739 TATATAAATAT-ATTAAAATTTATATAAA
1 TATATAAAAATAATTAAAAATAATATAAA
60767 TATATAAAAA-AATTAA
1 TATATAAAAATAATTAA
60783 TGAATATTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
27 16 0.25
28 37 0.57
29 2 0.03
30 10 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
TATATAAAAATAATTAAAAATAATATAAA
Found at i:60764 original size:20 final size:19
Alignment explanation
Indices: 60709--60775 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
60699 AATATAATAT
* *
60709 TATATAAAAATAATATAAA
1 TATATAAAATTTATATAAA
*
60728 AATAATATAAA--TATATAAA
1 TAT-ATA-AAATTTATATAAA
60747 TATATTAAAATTTATATAAA
1 TATA-TAAAATTTATATAAA
60767 TATATAAAA
1 TATATAAAA
60776 AAATTAATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.10
19 18 0.45
20 15 0.38
21 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TATATAAAATTTATATAAA
Found at i:61145 original size:12 final size:12
Alignment explanation
Indices: 61128--61196 Score: 58
Period size: 12 Copynumber: 6.2 Consensus size: 12
61118 TTACTCGAAT
* *
61128 TTTAAATTTTTA
1 TTTAAAATTTAA
61140 TTTAAAATTTAA
1 TTTAAAATTTAA
61152 TTT--AATTTAA
1 TTTAAAATTTAA
*
61162 TTTATAA-TTAA
1 TTTAAAATTTAA
* *
61173 -TAAAAATAT-A
1 TTTAAAATTTAA
61183 TTTAAAATTTAA
1 TTTAAAATTTAA
61195 TT
1 TT
61197 CAAATAAACT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
10 15 0.33
11 12 0.27
12 18 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTAAAATTTAA
Found at i:61165 original size:22 final size:23
Alignment explanation
Indices: 61138--61196 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
61128 TTTAAATTTT
* **
61138 TATTTAAAATTTAATTTAATTTA
1 TATTTAAAATTTAATTAAAAATA
*
61161 -ATTTATAA-TTAA-TAAAAATA
1 TATTTAAAATTTAATTAAAAATA
61181 TATTTAAAATTTAATT
1 TATTTAAAATTTAATT
61197 CAAATAAACT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 11 0.39
23 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTAAAATTTAATTAAAAATA
Found at i:61201 original size:22 final size:21
Alignment explanation
Indices: 61138--61202 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
61128 TTTAAATTTT
* *
61138 TATTTAAAATTTAATTTAATT
1 TATTTAAAATTTAATTAAATA
* *
61159 TAATTTATAA-TTAATAAAAATA
1 T-ATTTAAAATTTAAT-TAAATA
61181 TATTTAAAATTTAATTCAAATA
1 TATTTAAAATTTAATT-AAATA
61203 AACTAATCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTAAAATTTAATTAAATA
Found at i:61567 original size:14 final size:14
Alignment explanation
Indices: 61550--61577 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61540 TTAATATTTT
61550 TTAAAAAATATAAA
1 TTAAAAAATATAAA
61564 TTAAAAAATATAAA
1 TTAAAAAATATAAA
61578 AAAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAAAAATATAAA
Found at i:61919 original size:22 final size:22
Alignment explanation
Indices: 61894--61936 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
61884 ATAATTATTT
61894 TAAAAAAAT-AATATTTAATATA
1 TAAAAAAATAAATA-TTAATATA
61916 TAAAAAAATAAATATTAATAT
1 TAAAAAAATAAATATTAATAT
61937 TTATAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAAAATAAATATTAATATA
Found at i:66093 original size:17 final size:17
Alignment explanation
Indices: 66073--66132 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
66063 ATAAATATGT
66073 TATAAAAATAAATAAAA
1 TATAAAAATAAATAAAA
**
66090 TAT-ATTATAAAATAAAA
1 TATAAAAAT-AAATAAAA
*
66107 TATAAAATATTAATAATAA
1 TATAAAA-ATAAATAA-AA
66126 TTATAAA
1 -TATAAA
66133 TTAATTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 3 0.09
17 14 0.42
18 6 0.18
19 4 0.12
20 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAAAAATAAATAAAA
Found at i:66142 original size:19 final size:19
Alignment explanation
Indices: 66120--66180 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
66110 AAAATATTAA
66120 TAATAATTATAAATTAATT
1 TAATAATTATAAATTAATT
*
66139 TAATAATTTTAAATATAATT
1 TAATAATTATAAAT-TAATT
* * *
66159 AAATTA-TATTAAATAAATT
1 TAATAATTA-TAAATTAATT
66178 TAA
1 TAA
66181 ATTAAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATAATTATAAATTAATT
Found at i:66170 original size:20 final size:20
Alignment explanation
Indices: 66129--66184 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
66119 ATAATAATTA
* * *
66129 TAAAT-TAATTTAATAATTT
1 TAAATATAATTAAATTATAT
66148 TAAATATAATTAAATTATAT
1 TAAATATAATTAAATTATAT
66168 TAAATA-AATTTAAATTA
1 TAAATATAA-TTAAATTA
66185 AAAAATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.22
20 25 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATATAATTAAATTATAT
Found at i:66186 original size:15 final size:15
Alignment explanation
Indices: 66135--66196 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
66125 ATTATAAATT
* *
66135 AATTTAATAATTTTA
1 AATTAAATAAATTTA
*
66150 AATATAATTAAA-TTA
1 AAT-TAAATAAATTTA
*
66165 TATTAAATAAATTTA
1 AATTAAATAAATTTA
*
66180 AATTAAA-AAATTAA
1 AATTAAATAAATTTA
66194 AAT
1 AAT
66197 ATAATATAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
14 16 0.42
15 17 0.45
16 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAAATAAATTTA
Found at i:66231 original size:9 final size:11
Alignment explanation
Indices: 66062--66287 Score: 88
Period size: 11 Copynumber: 20.8 Consensus size: 11
66052 AATTATATTA
*
66062 TATAAATATGT
1 TATAAATATAT
*
66073 TATAAAAATA-
1 TATAAATATAT
*
66083 AATAAAATATAT
1 TAT-AAATATAT
* *
66095 TATAAAATAAAA
1 TAT-AAATATAT
66107 TATAAA-ATAT
1 TATAAATATAT
66117 TA-ATAATA-AT
1 TATA-AATATAT
66127 TATAAAT-TAAT
1 TATAAATAT-AT
66138 T-T-AATA-AT
1 TATAAATATAT
*
66146 TTTAAATATAAT
1 TATAAATAT-AT
*
66158 TA-AATTATAT
1 TATAAATATAT
*
66168 TAAATAAATTTAAAT
1 T--ATAAA--TATAT
66183 TA-AAA-A-AT
1 TATAAATATAT
*
66191 TA-AAATATAA
1 TATAAATATAT
*
66201 TATAATTATAT
1 TATAAATATAT
66212 TATAAATATAT
1 TATAAATATAT
66223 TATAAATATAT
1 TATAAATATAT
**
66234 ATCATTTATATAT
1 -T-ATAAATATAT
* *
66247 CA-AAAAATA-
1 TATAAATATAT
66256 TATAAATATAT
1 TATAAATATAT
*
66267 TACGTATATA-AT
1 TA--TAAATATAT
66279 TATAAATAT
1 TATAAATAT
66288 TATTTTTAAT
Statistics
Matches: 161, Mismatches: 27, Indels: 54
0.67 0.11 0.22
Matches are distributed among these distances:
8 10 0.06
9 8 0.05
10 41 0.25
11 57 0.35
12 24 0.15
13 16 0.10
15 5 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
TATAAATATAT
Found at i:66744 original size:16 final size:17
Alignment explanation
Indices: 66712--66753 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
66702 AAATTCTAAA
*
66712 AATTATAATTGTTTTAT
1 AATTATTATTGTTTTAT
66729 AATTATTATT-TTTTAT
1 AATTATTATTGTTTTAT
*
66745 AATAATTAT
1 AATTATTAT
66754 ATTTGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
AATTATTATTGTTTTAT
Found at i:67342 original size:2 final size:2
Alignment explanation
Indices: 67337--67372 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
67327 ACTAGGTGTG
*
67337 TA TA TA TA AA 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
67373 GAGGAATCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:67832 original size:8 final size:8
Alignment explanation
Indices: 67819--67844 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
67809 AGTTAGATTA
67819 TTTTAAAT
1 TTTTAAAT
67827 TTTTAAAT
1 TTTTAAAT
67835 TTTTAAAT
1 TTTTAAAT
67843 TT
1 TT
67845 AAATCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTAAAT
Found at i:67854 original size:16 final size:16
Alignment explanation
Indices: 67818--67873 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
67808 GAGTTAGATT
67818 ATTTTAAATTTTTAAAT-
1 ATTTTAAA--TTTAAATC
67835 -TTTTAAATTTAAATC
1 ATTTTAAATTTAAATC
*
67850 ATTTTAATTTTAAATC
1 ATTTTAAATTTAAATC
*
67866 ACTTTAAA
1 ATTTTAAA
67874 AATTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 7 0.21
16 27 0.79
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTAAATTTAAATC
Found at i:68882 original size:24 final size:25
Alignment explanation
Indices: 68827--68883 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
68817 TTTTATTTTT
68827 AATTATATTTTATATAATATAAATAA
1 AATTATA-TTTATATAATATAAATAA
* **
68853 AA-TATATTTATATTATAT-TTTAA
1 AATTATATTTATATAATATAAATAA
68876 AATTATAT
1 AATTATAT
68884 AATATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.19
24 16 0.59
25 4 0.15
26 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTATATTTATATAATATAAATAA
Found at i:71866 original size:2 final size:2
Alignment explanation
Indices: 71859--71895 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
71849 CAATATTGTG
71859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71896 GATTTCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:79220 original size:19 final size:20
Alignment explanation
Indices: 79184--79230 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
79174 AGATAAGAGT
*
79184 TGTTAATATTGATATTTA-A
1 TGTTAATATTAATATTTACA
*
79203 TGTTAATATTAATTTTTACA
1 TGTTAATATTAATATTTACA
*
79223 TGCTAATA
1 TGTTAATA
79231 CGAATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (20 bp):
TGTTAATATTAATATTTACA
Found at i:80552 original size:170 final size:171
Alignment explanation
Indices: 80349--80656 Score: 483
Period size: 170 Copynumber: 1.8 Consensus size: 171
80339 GCTTAAACTA
* * * * *
80349 AGCTTAAACTATACTAACTGAGCAATTTTTTGGCTATTACATATTTGAGCTTGTGACAATTCAGA
1 AGCTTAAACTATACTAACTGAGCAATCTTTTGGCTATTACATATTCGAGCCTGGGACAATTCACA
* * *
80414 AGTAGCATTGTATGCTTT-TTTTGGGTTCTAGGTTGCCGTAAAGTGCATGTTCAATGGCCTGAAA
66 AGTAGCATTGTATGCTTTCTTTTGGGCTCTAGGTTGCCGTAAAATGCATGTTCAATGCCCTGAAA
80478 TTTTATTTTATTTTATTTTTTGGTTGGCATTTCAAGTTTAG
131 TTTTATTTTATTTTATTTTTTGGTTGGCATTTCAAGTTTAG
* * * * *
80519 AGCTTAAGCTATAGTAACTGAGCAATCTTTTGGCTATTACGTATTCGAGCCTGGGATAATTGACA
1 AGCTTAAACTATACTAACTGAGCAATCTTTTGGCTATTACATATTCGAGCCTGGGACAATTCACA
*
80584 AGTAGGATTGTATGCTTTCTTTTGGGCTCTAGGTTGCCGTAAAATGCATGTTCAATGCCCTGAAA
66 AGTAGCATTGTATGCTTTCTTTTGGGCTCTAGGTTGCCGTAAAATGCATGTTCAATGCCCTGAAA
80649 TTTTATTT
131 TTTTATTT
80657 CTTTAGTCAC
Statistics
Matches: 123, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
170 72 0.59
171 51 0.41
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (171 bp):
AGCTTAAACTATACTAACTGAGCAATCTTTTGGCTATTACATATTCGAGCCTGGGACAATTCACA
AGTAGCATTGTATGCTTTCTTTTGGGCTCTAGGTTGCCGTAAAATGCATGTTCAATGCCCTGAAA
TTTTATTTTATTTTATTTTTTGGTTGGCATTTCAAGTTTAG
Found at i:82745 original size:29 final size:28
Alignment explanation
Indices: 82671--82753 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
82661 TTTGAATTAG
* *
82671 ATTTA-ATAATTTATATATT-TATATTAT
1 ATTTAGATATTTTATATATTATA-ATTTT
*
82698 ATTTATATATTTTATTATATTATAATTTT
1 ATTTAGATATTTTA-TATATTATAATTTT
82727 ATTTAAGATATTTTATATA-TA-AATTTT
1 ATTT-AGATATTTTATATATTATAATTTT
82754 GATCAATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 11 0.22
28 9 0.18
29 18 0.37
30 11 0.22
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
ATTTAGATATTTTATATATTATAATTTT
Found at i:83630 original size:30 final size:29
Alignment explanation
Indices: 83566--83630 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
83556 TATTAATATT
83566 TATATATTTTTATAATTAAATTTAAATAA
1 TATATATTTTTATAATTAAATTTAAATAA
*
83595 AATATATTTATTATAAATT-AA-TTATAATAA
1 TATATATTT-TTAT-AATTAAATTTA-AATAA
83625 TATATA
1 TATATA
83631 AATATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 11 0.35
30 16 0.52
31 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATATTTTTATAATTAAATTTAAATAA
Found at i:88513 original size:18 final size:17
Alignment explanation
Indices: 88477--88515 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
88467 TTACATGTTG
88477 AATATATATATATAGAT
1 AATATATATATATAGAT
88494 AATATA-ATATATCAGTAT
1 AATATATATATAT-AG-AT
88512 AATA
1 AATA
88516 GGTATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (17 bp):
AATATATATATATAGAT
Found at i:94326 original size:15 final size:16
Alignment explanation
Indices: 94292--94335 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
94282 CCAAACACAA
*
94292 CCCCAACCCACCACCACC
1 CCCCCACCC-CCA-CACC
94310 CCCCC-CCCCCACACC
1 CCCCCACCCCCACACC
94325 CCCCCACCCCC
1 CCCCCACCCCC
94336 CAACCCACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 8 0.33
17 3 0.12
18 4 0.17
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (16 bp):
CCCCCACCCCCACACC
Found at i:94394 original size:9 final size:9
Alignment explanation
Indices: 94380--94441 Score: 63
Period size: 10 Copynumber: 6.6 Consensus size: 9
94370 CCGGACCGAA
94380 CCACCCCCC
1 CCACCCCCC
94389 CCACCCCCC
1 CCACCCCCC
*
94398 GCACGCCACCC
1 CCAC-CC-CCC
*
94409 CCGACACCCC
1 CC-ACCCCCC
94419 CC-CCCCCC
1 CCACCCCCC
94427 CCACCGCCCC
1 CCACC-CCCC
94437 CCACC
1 CCACC
94442 ACCCGCCCCC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 7 0.16
9 14 0.32
10 16 0.36
11 5 0.11
12 2 0.05
ACGTcount: A:0.13, C:0.81, G:0.06, T:0.00
Consensus pattern (9 bp):
CCACCCCCC
Found at i:99914 original size:18 final size:18
Alignment explanation
Indices: 99887--99928 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
99877 AGGGTTTTTG
99887 CCCCCCGG-CCGCCGTCC
1 CCCCCCGGCCCGCCGTCC
*
99904 CCCCGCCGGCCCGCCTTCC
1 CCCC-CCGGCCCGCCGTCC
99923 CCCCCC
1 CCCCCC
99929 TTTCTACCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 12 0.55
ACGTcount: A:0.00, C:0.74, G:0.19, T:0.07
Consensus pattern (18 bp):
CCCCCCGGCCCGCCGTCC
Found at i:103171 original size:13 final size:14
Alignment explanation
Indices: 103153--103184 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
103143 AAAAAATAAA
103153 TAAAATTTTAA-TT
1 TAAAATTTTAATTT
103166 TAAAATTTTAATTT
1 TAAAATTTTAATTT
103180 TAAAA
1 TAAAA
103185 AACATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAATTTTAATTT
Found at i:103454 original size:45 final size:46
Alignment explanation
Indices: 103365--103464 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 46
103355 TAATTAAATA
* * *
103365 TTAATTTTAATTTTATTAAAAATAATAATAATAAATCTTTTTAAT-
1 TTAATTTTTATTTTATAAAAAATAATAATAATAAATCTTATTAATG
* *
103410 TTAATTTTTATTTTA-AAAAAATAATTAATATTTTAAT-TTATTAATG
1 TTAATTTTTATTTTATAAAAAATAA-TAATA-ATAAATCTTATTAATG
*
103456 TAAATTTTT
1 TTAATTTTT
103465 TTAAAGTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
44 8 0.17
45 26 0.57
46 12 0.26
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (46 bp):
TTAATTTTTATTTTATAAAAAATAATAATAATAAATCTTATTAATG
Found at i:103464 original size:116 final size:118
Alignment explanation
Indices: 103158--103510 Score: 372
Period size: 116 Copynumber: 3.0 Consensus size: 118
103148 ATAAATAAAA
*
103158 TTTTAATTTAAAATTTTAATTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGT-AA-T
1 TTTTAATTT-AAATTTTTATTTT-AAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATT
* * *
103221 TTTT-AAC-TAATTAAATATT-TTTTATTTTATTAAAAAATTACAATAAAAAACCT
64 TTTTAAACTTAATTAAATATTATTTTATTTTATT-AAAAATAATAATAATAAACCT
*
103274 TTTTATTTTATTTAAATTTTTTTATTTTTATAAAAATATAATAATTAATATTTTAATTTGTTAAT
1 TTTTA----ATTTAAA--TTTTTA--TTT-TAAAAACATAATAATTAATATTTTAATTTGTTAAT
* * *
103339 ATAATTTTTTTAAACTTAATTAAATATTAATTTTAATTTTATTAAAAATAATAATAATAAATCT
57 GTAAATTTTTTAAACTTAATTAAATATT-ATTTT-ATTTTATTAAAAATAATAATAATAAACCT
*
103403 TTTTAATTT-AATTTTTATTTT-AAAA-A-AATAATTAATATTTTAATTTATTAATGTAAATTTT
1 TTTTAATTTAAATTTTTATTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAA-TTT
*
103464 TTTAAAGTTAATT-AATATTATTTT-TTGTTA--AAAAATAATAATTAATA
65 TTTAAACTTAATTAAATATTATTTTATT-TTATTAAAAATAATAA-TAATA
103511 CATTATATTT
Statistics
Matches: 206, Mismatches: 12, Indels: 41
0.80 0.05 0.16
Matches are distributed among these distances:
112 11 0.05
113 7 0.03
114 3 0.01
115 5 0.02
116 39 0.19
117 16 0.08
118 4 0.02
119 4 0.02
120 7 0.03
121 5 0.02
122 6 0.03
123 37 0.18
124 4 0.02
125 9 0.04
126 3 0.01
127 12 0.06
129 26 0.13
130 8 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (118 bp):
TTTTAATTTAAATTTTTATTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTT
TTAAACTTAATTAAATATTATTTTATTTTATTAAAAATAATAATAATAAACCT
Found at i:103799 original size:63 final size:63
Alignment explanation
Indices: 103732--103853 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 63
103722 AAAAAAGCCT
* *
103732 AAAAAATATACATGTTTATTTTTTATTTGTA-TTTTTATTATTTAAAATATTATAAATTTGAC
1 AAAAAAAATACATGTTTATTTTTTATTTATATTTTTTATTATTTAAAATATTATAAATTTGAC
** *
103794 AAAAAAAATTTATGTTTATTTTTTGTTTATATTTTTTATTATTTAAAATATTATAAATTT
1 AAAAAAAATACATGTTTATTTTTTATTTATATTTTTTATTATTTAAAATATTATAAATTT
103854 AGATAATATT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 26 0.48
63 28 0.52
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (63 bp):
AAAAAAAATACATGTTTATTTTTTATTTATATTTTTTATTATTTAAAATATTATAAATTTGAC
Found at i:103877 original size:60 final size:60
Alignment explanation
Indices: 103748--103879 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 60
103738 TATACATGTT
* ***
103748 TATTTTTTATTTGTATTTTTATTATTTAAAATATTATAAATTTGACAAAAAAAATTTATGTT
1 TATTTTTTATTTATATTTTTATTATTTAAAATATTATAAATTT-A-AAAAAAAATTTATAAA
* * * *
103810 TATTTTTTGTTTATATTTTTTATTATTTAAAATATTATAAATTT-AGATAATATTTATAAA
1 TATTTTTTATTTATA-TTTTTATTATTTAAAATATTATAAATTTAAAAAAAAATTTATAAA
103870 TATTTTTTAT
1 TATTTTTTAT
103880 ATTTTTATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
60 19 0.32
62 13 0.22
63 28 0.47
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (60 bp):
TATTTTTTATTTATATTTTTATTATTTAAAATATTATAAATTTAAAAAAAAATTTATAAA
Found at i:103950 original size:24 final size:24
Alignment explanation
Indices: 103895--103956 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
103885 TATATTCATG
* * *
103895 TCATATTTATTTTTTATATTTTGT
1 TCATATTAATTTTTAATATTGTGT
*
103919 T-TTAATTAATTTTTAATATTGTGT
1 TCAT-ATTAATTTTTAATATTGTGT
*
103943 TCATATTATTTTTT
1 TCATATTAATTTTT
103957 GTATATATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (24 bp):
TCATATTAATTTTTAATATTGTGT
Found at i:103953 original size:23 final size:22
Alignment explanation
Indices: 103879--103955 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 22
103869 ATATTTTTTA
103879 TATTTTTATATTCATG-TCATATT
1 TATTTTTATATT-ATGTTCATA-T
* *
103902 TATTTTTTATATTTTGTT-TTAAT
1 TA-TTTTTATATTATGTTCAT-AT
*
103925 TAATTTTTAATATTGTGTTCATAT
1 T-ATTTTT-ATATTATGTTCATAT
103949 TATTTTT
1 TATTTTT
103956 TGTATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
23 18 0.41
24 25 0.57
25 1 0.02
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.66
Consensus pattern (22 bp):
TATTTTTATATTATGTTCATAT
Found at i:105234 original size:9 final size:9
Alignment explanation
Indices: 105216--105279 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
105206 GGAACGACAA
105216 AAAG-AAAG
1 AAAGAAAAG
105224 AAAGAAAAG
1 AAAGAAAAG
*
105233 AAAAAGAAAGG
1 --AAAGAAAAG
105244 AAAGAGAAAG
1 AAAGA-AAAG
*
105254 AAAAAAAAG
1 AAAGAAAAG
*
105263 AAAGGAAAG
1 AAAGAAAAG
*
105272 AGAGAAAA
1 AAAGAAAA
105280 AATATGTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
8 4 0.09
9 26 0.58
10 7 0.16
11 8 0.18
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:105240 original size:15 final size:15
Alignment explanation
Indices: 105220--105265 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
105210 CGACAAAAAG
105220 AAAGAAAGAAAAGAA
1 AAAGAAAGAAAAGAA
* *
105235 AAAGAAAGGAAAGAG
1 AAAGAAAGAAAAGAA
*
105250 AAAGAAAAAAAAGAA
1 AAAGAAAGAAAAGAA
105265 A
1 A
105266 GGAAAGAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Found at i:105247 original size:24 final size:23
Alignment explanation
Indices: 105219--105281 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
105209 ACGACAAAAA
105219 GAAAGAAAGAAAAGAAAAAGAAAG
1 GAAAGAAAGAAAA-AAAAAGAAAG
105243 GAAAGAGAA-AGAAAAAAAAGAAAG
1 GAAAGA-AAGA-AAAAAAAAGAAAG
*
105267 GAAAGAGAGAAAAAA
1 GAAAGAAAGAAAAAA
105282 TATGTTTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 6 0.17
24 24 0.69
25 5 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (23 bp):
GAAAGAAAGAAAAAAAAAGAAAG
Found at i:105353 original size:16 final size:14
Alignment explanation
Indices: 105334--105369 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
105324 ATTATAAATT
*
105334 TATATAATATTTTA
1 TATATATTATTTTA
105348 TATATATTATTTTA
1 TATATATTATTTTA
*
105362 TACATATT
1 TATATATT
105370 TAACATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATATTATTTTA
Found at i:105401 original size:16 final size:17
Alignment explanation
Indices: 105368--105405 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
105358 TTTATACATA
**
105368 TTTAACATATATTTATT
1 TTTAACATATATAAATT
105385 TTTAAC-TATATAAATT
1 TTTAACATATATAAATT
105401 TTTAA
1 TTTAA
105406 TACGCTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAACATATATAAATT
Found at i:106704 original size:33 final size:33
Alignment explanation
Indices: 106662--106724 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
106652 GTGTTTAGAA
106662 TAATAAAATTTCACATAAACTCAAAAAACAGAG
1 TAATAAAATTTCACATAAACTCAAAAAACAGAG
* *
106695 TAATAAAATTTCACATAATCTCACAAAACA
1 TAATAAAATTTCACATAAACTCAAAAAACA
106725 ATTAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.56, C:0.17, G:0.03, T:0.24
Consensus pattern (33 bp):
TAATAAAATTTCACATAAACTCAAAAAACAGAG
Done.