Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2754
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: 83988
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:3578 original size:13 final size:13
Alignment explanation
Indices: 3560--3585 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3550 ACATTTGGTC
3560 ATGTATCGATACA
1 ATGTATCGATACA
3573 ATGTATCGATACA
1 ATGTATCGATACA
3586 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3580 original size:33 final size:32
Alignment explanation
Indices: 3538--3605 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
3528 CGTTACAAAC
3538 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
3571 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
3603 CAA
1 CAA
3606 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:3692 original size:13 final size:13
Alignment explanation
Indices: 3674--3698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3664 TACAGTGGTC
3674 ATGTATCGATACA
1 ATGTATCGATACA
3687 ATGTATCGATAC
1 ATGTATCGATAC
3699 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4332 original size:22 final size:22
Alignment explanation
Indices: 4307--4378 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
4297 AAATATAAAT
4307 TTAAACTTAAACCCAAACCCAA
1 TTAAACTTAAACCCAAACCCAA
** ** ** *
4329 TTAAAAC-CCAACTAAAAATCTA
1 TT-AAACTTAAACCCAAACCCAA
4351 TATAAACTTAAACCCAAACCCAA
1 T-TAAACTTAAACCCAAACCCAA
4374 TTAAA
1 TTAAA
4379 ACCTAATTAA
Statistics
Matches: 33, Mismatches: 14, Indels: 6
0.62 0.26 0.11
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (22 bp):
TTAAACTTAAACCCAAACCCAA
Found at i:4358 original size:45 final size:45
Alignment explanation
Indices: 4308--4425 Score: 200
Period size: 45 Copynumber: 2.6 Consensus size: 45
4298 AATATAAATT
4308 TAAACTTAAACCCAAACCCAATTAAAACCCAACTAAAAATCTATA
1 TAAACTTAAACCCAAACCCAATTAAAACCCAACTAAAAATCTATA
* *
4353 TAAACTTAAACCCAAACCCAATTAAAACCTAATTAAAAATCTATA
1 TAAACTTAAACCCAAACCCAATTAAAACCCAACTAAAAATCTATA
*
4398 TAAACTTAAACCCAAACCAAATTTAAAA
1 TAAACTTAAACCCAAACCCAA-TTAAAA
4426 AAAACTCAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 63 0.91
46 6 0.09
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (45 bp):
TAAACTTAAACCCAAACCCAATTAAAACCCAACTAAAAATCTATA
Found at i:5978 original size:29 final size:29
Alignment explanation
Indices: 5936--5997 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
5926 TTGCATGGTA
*
5936 AAAATAATAATATTTTAATAACTT-ATTTT
1 AAAACAATAATATTTTAATAA-TTAATTTT
*
5965 AAAACAATATTATTTTAATAATTAATTTT
1 AAAACAATAATATTTTAATAATTAATTTT
5994 AAAA
1 AAAA
5998 ATAACAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAACAATAATATTTTAATAATTAATTTT
Found at i:6932 original size:2 final size:2
Alignment explanation
Indices: 6925--6959 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6915 ATTAAAAGTA
6925 AT 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 AT A
6960 GAAATTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7688 original size:20 final size:20
Alignment explanation
Indices: 7624--7689 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
7614 TTTATTAATG
7624 ATTTAATATATTTAAAA-TTT
1 ATTTAA-ATATTTAAAATTTT
* *
7644 ATTT-ACT-GTT-AAATTATT
1 ATTTAAATATTTAAAATT-TT
*
7662 -TTAAAATATTTAAAATTTT
1 ATTTAAATATTTAAAATTTT
7681 ATTTAAATA
1 ATTTAAATA
7690 AATTGATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
16 3 0.09
17 5 0.15
18 5 0.15
19 5 0.15
20 16 0.47
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTAAATATTTAAAATTTT
Found at i:8036 original size:21 final size:21
Alignment explanation
Indices: 8012--8073 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
8002 ATATATATAA
8012 ATTTTAATAATTTAAATTATT
1 ATTTTAATAATTTAAATTATT
* **
8033 ATTTAAATAATAAAAATTTATT
1 ATTTTAATAATTTAAA-TTATT
*
8055 TTTATTAA-AATTT-AATTAT
1 ATT-TTAATAATTTAAATTAT
8074 AAAAATTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
20 4 0.12
21 15 0.47
22 10 0.31
23 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTAATAATTTAAATTATT
Found at i:8050 original size:36 final size:37
Alignment explanation
Indices: 7976--8051 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 37
7966 AAATTAATTT
* * *
7976 TTTTAAATAAATTTAATTTTTATTTTATATATATAAA
1 TTTTAAATAAATTTAATTATTATTTAATATATAAAAA
8013 TTTT-AAT-AATTTAAATTATTATTTAA-ATAATAAAAA
1 TTTTAAATAAATTT-AATTATTATTTAATAT-ATAAAAA
8049 TTT
1 TTT
8052 ATTTTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 7 0.21
36 23 0.68
37 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
TTTTAAATAAATTTAATTATTATTTAATATATAAAAA
Found at i:8078 original size:14 final size:14
Alignment explanation
Indices: 8042--8091 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 14
8032 TATTTAAATA
*
8042 ATAAAAATTTATTTTT
1 ATAAAAATTTA--ATT
*
8058 ATTAAAATTTAATT
1 ATAAAAATTTAATT
8072 ATAAAAA-TTAA-T
1 ATAAAAATTTAATT
8084 ATAAAAAT
1 ATAAAAAT
8092 AATTTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 8 0.27
13 4 0.13
14 8 0.27
16 10 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAAAATTTAATT
Found at i:12357 original size:24 final size:24
Alignment explanation
Indices: 12328--12378 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
12318 AGTATATCAG
12328 TTATTAATAAAGGTAGTTTGTTTA
1 TTATTAATAAAGGTAGTTTGTTTA
12352 TTATTAATAAAGGTAGTTTGTTTA
1 TTATTAATAAAGGTAGTTTGTTTA
12376 TTA
1 TTA
12379 ATCAAGTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (24 bp):
TTATTAATAAAGGTAGTTTGTTTA
Found at i:13628 original size:23 final size:22
Alignment explanation
Indices: 13594--13636 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
13584 ATTAATAAGA
*
13594 ATTTTCATTAAATATTATAAATT
1 ATTTTCATTAAA-AATATAAATT
13617 ATTTT-ATATAAAAATATAAA
1 ATTTTCAT-TAAAAATATAAA
13637 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTTCATTAAAAATATAAATT
Found at i:13691 original size:29 final size:29
Alignment explanation
Indices: 13628--13689 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
13618 TTTTATATAA
* *
13628 AAATATAA-AAAATAAAAATATAGTAATG
1 AAATTTAATAAAATAAAAATATAATAATG
* *
13656 AAATTTAATAAAATTAAAATATAATGAT-
1 AAATTTAATAAAATAAAAATATAATAATG
13684 AAATTT
1 AAATTT
13690 TATATTGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATTTAATAAAATAAAAATATAATAATG
Found at i:14087 original size:20 final size:20
Alignment explanation
Indices: 14048--14096 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
14038 AAATTATATT
**
14048 TTAATTAAATCGATTTAAAA
1 TTAATTAAATCGATAAAAAA
*
14068 TTAATTCAATCGATAAAAAAA
1 TTAATTAAATCGAT-AAAAAA
14089 TT-ATTAAA
1 TTAATTAAA
14097 ATAATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (20 bp):
TTAATTAAATCGATAAAAAA
Found at i:14310 original size:17 final size:18
Alignment explanation
Indices: 14283--14317 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
14273 TATTTAAAAT
14283 TTTATTTAAATAAATTAA
1 TTTATTTAAATAAATTAA
*
14301 TTTA-TTAAATTAATTAA
1 TTTATTTAAATAAATTAA
14318 ATTAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATTTAAATAAATTAA
Found at i:14559 original size:7 final size:7
Alignment explanation
Indices: 14547--14572 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
14537 TAGAGACACG
14547 TTAAAAT
1 TTAAAAT
14554 TTAAAAT
1 TTAAAAT
14561 TTAAAAT
1 TTAAAAT
14568 TTAAA
1 TTAAA
14573 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAAAT
Found at i:14605 original size:21 final size:20
Alignment explanation
Indices: 14581--14638 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 20
14571 AATAAAAAAA
14581 TTATAAATTAAATTTATTTAT
1 TTATAAATT-AATTTATTTAT
14602 TTATTAAA-TAATTTATTTGAT
1 TTA-TAAATTAATTTATTT-AT
14623 TTAATAAATTTAATTT
1 TT-ATAAA-TTAATTT
14639 TTATTTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 9 0.28
21 12 0.38
22 5 0.16
23 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATAAATTAATTTATTTAT
Found at i:14616 original size:20 final size:21
Alignment explanation
Indices: 14591--14631 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
14581 TTATAAATTA
*
14591 AATTTATTT-ATTTATTAAAT
1 AATTTATTTGATTTAATAAAT
14611 AATTTATTTGATTTAATAAAT
1 AATTTATTTGATTTAATAAAT
14632 TTAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTTATTTGATTTAATAAAT
Found at i:14646 original size:20 final size:20
Alignment explanation
Indices: 14589--14647 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
14579 AATTATAAAT
* *
14589 TAAATTTATTTATTTATTAAA
1 TAAATTTAATT-TTTATTTAA
*
14610 T-AATTT-A-TTTGATTTAA
1 TAAATTTAATTTTTATTTAA
14627 TAAATTTAATTTTTATTTAA
1 TAAATTTAATTTTTATTTAA
14647 T
1 T
14648 GTATAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 8 0.26
18 6 0.19
19 1 0.03
20 15 0.48
21 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TAAATTTAATTTTTATTTAA
Found at i:19331 original size:18 final size:18
Alignment explanation
Indices: 19310--19373 Score: 71
Period size: 16 Copynumber: 3.7 Consensus size: 18
19300 TTTATTATTT
*
19310 AATTTTAAATTATTTTAA
1 AATTTTAAATTAATTTAA
*
19328 AA--TTAAGTTAATTTAA
1 AATTTTAAATTAATTTAA
*
19344 AATTTTAAATCAATTT-A
1 AATTTTAAATTAATTTAA
*
19361 AATTTTAATTTAA
1 AATTTTAAATTAA
19374 ATAAATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 14 0.37
17 12 0.32
18 12 0.32
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
AATTTTAAATTAATTTAA
Found at i:19365 original size:17 final size:17
Alignment explanation
Indices: 19306--19373 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
19296 ATTTTTTATT
19306 ATTT-AATTTTAAATTA
1 ATTTAAATTTTAAATTA
* * *
19322 TTTTAAA-ATTAAGTTA
1 ATTTAAATTTTAAATTA
*
19338 ATTTAAAATTTTAAATCA
1 ATTT-AAATTTTAAATTA
*
19356 ATTTAAATTTTAATTTA
1 ATTTAAATTTTAAATTA
19373 A
1 A
19374 ATAAATCAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
16 13 0.32
17 17 0.43
18 10 0.25
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTTAAATTA
Found at i:19675 original size:2 final size:2
Alignment explanation
Indices: 19668--19703 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19658 TCCACTTTCA
19668 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
19704 GACCATGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20038 original size:23 final size:22
Alignment explanation
Indices: 20004--20046 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
19994 ATTAATATAA
*
20004 ATTTTCATTAAACATTATAAATT
1 ATTTTCATTAAA-AATATAAATT
20027 ATTTT-ATATAAAAATATAAA
1 ATTTTCAT-TAAAAATATAAA
20047 AATAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTTCATTAAAAATATAAATT
Found at i:20078 original size:16 final size:14
Alignment explanation
Indices: 20056--20097 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
20046 AAATAAAATG
20056 ATAAAATTTAATAAA
1 ATAAAATTTAAT-AA
*
20071 ACTAAAATTTAGT-A
1 A-TAAAATTTAATAA
20085 ATAAAATTTAATA
1 ATAAAATTTAATA
20098 TTAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 1 0.04
16 10 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
ATAAAATTTAATAA
Found at i:20432 original size:18 final size:18
Alignment explanation
Indices: 20411--20445 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20401 ATAATATCTA
*
20411 TATAATATTTAATAAAAT
1 TATAATATTAAATAAAAT
20429 TATAATATTAAATAAAA
1 TATAATATTAAATAAAA
20446 ATATTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAATATTAAATAAAAT
Found at i:20698 original size:2 final size:2
Alignment explanation
Indices: 20691--20723 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20681 TATCATACTC
20691 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 T
20724 GGAAATTAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22166 original size:173 final size:173
Alignment explanation
Indices: 21877--22219 Score: 634
Period size: 173 Copynumber: 2.0 Consensus size: 173
21867 CAAAGACAAA
21877 CATGAAGCAATAAATAAGGGTTCGCACAAGGACGATCGAAACACCCGAAGCCAATCGGAACTTTT
1 CATGAAGCAATAAATAAGGGTTCGCACAAGGACGATCGAAACACCCGAAGCCAATCGGAACTTTT
*
21942 CGACGATTGAAGGCAGGTAGCAGTTTTCGAACGATATGATCTTAAGAGAAGACTTTAAAAAGAAG
66 CGACGATTGAAGGCAGGTAGCAGTTTTCGAACGATAGGATCTTAAGAGAAGACTTTAAAAAGAAG
*
22007 GAAGAAGGAAAGAAAGAAGAAAGATAAGGTTGTAGCAGTTGAG
131 GAAGAAAGAAAGAAAGAAGAAAGATAAGGTTGTAGCAGTTGAG
22050 CATGAAGCAATAAATAAGGGTTCGCACAAGGACGA-CGGAAACACCCGAAGCCAATCGGAACTTT
1 CATGAAGCAATAAATAAGGGTTCGCACAAGGACGATC-GAAACACCCGAAGCCAATCGGAACTTT
*
22114 TCGACGATTGAAGGCAGGTAGCAGTTTTCGAACGATAGGATCTTAAGAGAAGACTTTAAAAGGAA
65 TCGACGATTGAAGGCAGGTAGCAGTTTTCGAACGATAGGATCTTAAGAGAAGACTTTAAAAAGAA
*
22179 GGAAGAAAGAAAGCAAGAAGAAAGATAAGGTTGTAGCAGTT
130 GGAAGAAAGAAAGAAAGAAGAAAGATAAGGTTGTAGCAGTT
22220 AAGAAAGAAT
Statistics
Matches: 165, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
172 1 0.01
173 164 0.99
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (173 bp):
CATGAAGCAATAAATAAGGGTTCGCACAAGGACGATCGAAACACCCGAAGCCAATCGGAACTTTT
CGACGATTGAAGGCAGGTAGCAGTTTTCGAACGATAGGATCTTAAGAGAAGACTTTAAAAAGAAG
GAAGAAAGAAAGAAAGAAGAAAGATAAGGTTGTAGCAGTTGAG
Found at i:22462 original size:21 final size:21
Alignment explanation
Indices: 22438--22480 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
22428 TTTTAACTCA
22438 AATTATTTCAAATTTAAAAAT
1 AATTATTTCAAATTTAAAAAT
* *
22459 AATTATTTTAAATTTAATAAT
1 AATTATTTCAAATTTAAAAAT
22480 A
1 A
22481 TCACATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTATTTCAAATTTAAAAAT
Found at i:22514 original size:16 final size:15
Alignment explanation
Indices: 22490--22548 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
22480 ATCACATAAA
22490 ATTTAATTTTTAAATT
1 ATTTAA-TTTTAAATT
*
22506 ATTTGATTTTAAATT
1 ATTTAATTTTAAATT
*
22521 ATTTTAAATTT-AATT
1 A-TTTAATTTTAAATT
* *
22536 ATTGAGTTTTAAA
1 ATTTAATTTTAAA
22549 ATTAAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 6 0.17
15 17 0.49
16 12 0.34
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (15 bp):
ATTTAATTTTAAATT
Found at i:22789 original size:2 final size:2
Alignment explanation
Indices: 22782--22809 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22772 CATTTTCTAC
22782 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
22810 GAACATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23154 original size:19 final size:19
Alignment explanation
Indices: 23133--23169 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23123 TAAAACTAAA
23133 AAAAT-TAATAATAAAATT
1 AAAATATAATAATAAAATT
*
23151 AAAATATAATGATAAAATT
1 AAAATATAATAATAAAATT
23170 TAATATTAAA
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATATAATAATAAAATT
Found at i:23523 original size:42 final size:42
Alignment explanation
Indices: 23409--23524 Score: 110
Period size: 42 Copynumber: 2.7 Consensus size: 42
23399 TTAGCTCAAA
* *
23409 TAAATATTTTATATTAAATATATAAATATTAATATTTAATAAAAT
1 TAAATATTATA-ATTAAATAT-T-AATATTAATATTTAAAAAAAT
* * * * *
23454 TATAATACTA-AGTAAAATATTATTATTATTATTTAAAAAATAT
1 TA-AATATTATAATTAAATATTAATATTAATATTTAAAAAA-AT
23497 TAAATATTATAATTAAAT-TTAATATTAA
1 TAAATATTATAATTAAATATTAATATTAA
23525 ATATCATATT
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
42 30 0.54
43 11 0.20
44 7 0.12
45 3 0.05
46 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (42 bp):
TAAATATTATAATTAAATATTAATATTAATATTTAAAAAAAT
Found at i:23525 original size:12 final size:12
Alignment explanation
Indices: 23492--23542 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
23482 TTATTTAAAA
23492 AATATTAAATATT
1 AATATTAAAT-TT
23505 -ATAATTAAATTT
1 AAT-ATTAAATTT
*
23517 AATATTAAATAT
1 AATATTAAATTT
*
23529 CATATTAATATTT
1 AATATTAA-ATTT
23542 A
1 A
23543 TTTAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 19 0.61
13 12 0.39
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATTAAATTT
Found at i:23526 original size:25 final size:25
Alignment explanation
Indices: 23492--23542 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
23482 TTATTTAAAA
*
23492 AATATTAAATATTATAATTAA-ATTT
1 AATATTAAATATCAT-ATTAATATTT
23517 AATATTAAATATCATATTAATATTT
1 AATATTAAATATCATATTAATATTT
23542 A
1 A
23543 TTTAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
AATATTAAATATCATATTAATATTT
Found at i:23549 original size:22 final size:20
Alignment explanation
Indices: 23519--23559 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
23509 TTAAATTTAA
23519 TATTAAATATCATATTAATATT
1 TATTAAATA--ATATTAATATT
*
23541 TATTTAATAATATTAATAT
1 TATTAAATAATATTAATAT
23560 AAAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTAAATAATATTAATATT
Found at i:23553 original size:14 final size:14
Alignment explanation
Indices: 23534--23573 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
23524 AATATCATAT
*
23534 TAATATTTATTTAA
1 TAATATTTATATAA
*
23548 TAATATTAATATAA
1 TAATATTTATATAA
23562 -AATATTTATATA
1 TAATATTTATATA
23574 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTTATATAA
Found at i:23576 original size:31 final size:30
Alignment explanation
Indices: 23536--23629 Score: 86
Period size: 31 Copynumber: 3.0 Consensus size: 30
23526 TATCATATTA
* *
23536 ATATTTATTTAATAATA-T-TAATATAAAAT
1 ATATATATTTAATAAAATTATAATAT-AAAT
23565 ATTTATATATTTAATAAAATTATAATATAAAT
1 A--TATATATTTAATAAAATTATAATATAAAT
23597 ATATAT-TTTAATAAATATATTATATATATAAAT
1 ATATATATTTAAT-AA-A-ATTATA-ATATAAAT
23630 TAAGACTCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
29 7 0.13
30 7 0.13
31 15 0.27
32 12 0.22
33 14 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATATATATTTAATAAAATTATAATATAAAT
Found at i:23588 original size:28 final size:29
Alignment explanation
Indices: 23557--23611 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
23547 ATAATATTAA
**
23557 TATAAAATATTTATATA-TTTAATAAAAT
1 TATAAAATAAATATATATTTTAATAAAAT
*
23585 TATAATATAAATATATATTTTAATAAA
1 TATAAAATAAATATATATTTTAATAAA
23612 TATATTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TATAAAATAAATATATATTTTAATAAAAT
Found at i:23818 original size:36 final size:36
Alignment explanation
Indices: 23739--23829 Score: 91
Period size: 36 Copynumber: 2.5 Consensus size: 36
23729 TATCGTTTTT
23739 ATAATAAAAATATTTTTATTTAAATTTAATATTATAA
1 ATAATAAAAATATTTTTA-TTAAATTTAATATTATAA
*
23776 AT-ATAAAAA-A-TTTTA-TAATATTTAATATAGTTTAA
1 ATAATAAAAATATTTTTATTAA-ATTTAATAT--TATAA
*
23811 ATAATAAAATAAATTTTTA
1 ATAATAAAA-ATATTTTTA
23830 GATTATTTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
32 3 0.07
33 9 0.20
34 5 0.11
35 7 0.15
36 13 0.28
37 3 0.07
38 1 0.02
39 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (36 bp):
ATAATAAAAATATTTTTATTAAATTTAATATTATAA
Found at i:23829 original size:39 final size:36
Alignment explanation
Indices: 23739--23829 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 36
23729 TATCGTTTTT
*
23739 ATAATAAAAATATTTTTATTTAAATTTAATATTATAA
1 ATAATAAAAAAATTTTTA-TTAAATTTAATATTATAA
*
23776 AT-AT-AAAAAA-TTTTA-TAATATTTAATATAGTTTAA
1 ATAATAAAAAAATTTTTATTAA-ATTTAATAT--TATAA
23811 ATAATAAAATAAATTTTTA
1 ATAATAAAA-AAATTTTTA
23830 GATTATTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
32 3 0.07
33 9 0.20
34 5 0.11
35 11 0.24
36 4 0.09
37 5 0.11
38 3 0.07
39 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (36 bp):
ATAATAAAAAAATTTTTATTAAATTTAATATTATAA
Found at i:24486 original size:2 final size:2
Alignment explanation
Indices: 24479--24514 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
24469 ATTTTGCCTC
24479 AT AT AT AT AT AT AT AT AT A- ACT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
24515 TGTTTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24671 original size:50 final size:50
Alignment explanation
Indices: 24617--24715 Score: 114
Period size: 50 Copynumber: 2.0 Consensus size: 50
24607 TACATTAAAA
*
24617 ATATTTATAAATCAAA-TTAAATTATA-ATAAAAA-TAATTTTTATTTTTTAT
1 ATATTTA-AAATCAAATTTAAATTA-ACATAAAAATTAA-TTTTATTATTTAT
* * *
24667 ATATTTAAATTTAAATTTAAATTAACTTAAAAATTAATTTTATTATTTA
1 ATATTTAAAATCAAATTTAAATTAACATAAAAATTAATTTTATTATTTA
24716 AAAAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
49 7 0.17
50 32 0.76
51 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
ATATTTAAAATCAAATTTAAATTAACATAAAAATTAATTTTATTATTTAT
Found at i:24751 original size:18 final size:18
Alignment explanation
Indices: 24695--24752 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
24685 AAATTAACTT
24695 AAAAATTAATTTTATTATTTA
1 AAAAATT-ATTTTA-TA-TTA
* ** *
24716 AAAAAATATTAAAAATTA
1 AAAAATTATTTTATATTA
24734 AAAAATTATTTTATATTA
1 AAAAATTATTTTATATTA
24752 A
1 A
24753 TAATTAATAA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
18 18 0.62
19 1 0.03
20 4 0.14
21 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAATTATTTTATATTA
Found at i:24795 original size:17 final size:19
Alignment explanation
Indices: 24751--24796 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
24741 ATTTTATATT
24751 AATAATTAATAATTAATTTA
1 AATAA-TAATAATTAATTTA
24771 AA-ATATAA-AATT-ATTTA
1 AATA-ATAATAATTAATTTA
24788 AATAATAAT
1 AATAATAAT
24797 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
17 11 0.48
18 5 0.22
19 4 0.17
20 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAATAATAATTAATTTA
Found at i:42682 original size:9 final size:9
Alignment explanation
Indices: 42670--42708 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
42660 TTAATTGAAA
42670 AAATTAATT
1 AAATTAATT
42679 AAATTAAATT
1 AAATT-AATT
*
42689 TAATTAATT
1 AAATTAATT
*
42698 TAATTAATT
1 AAATTAATT
42707 AA
1 AA
42709 GTCTAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAATTAATT
Found at i:42883 original size:23 final size:23
Alignment explanation
Indices: 42852--42926 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
42842 TAAATCTATT
*
42852 TAAATCTAAATTAAAAG-TTCATC
1 TAAAACTAAATTAAAAGCTT-ATC
* *
42875 TAAACCTAAATTAAAAGCTTATT
1 TAAAACTAAATTAAAAGCTTATC
* *
42898 TAAAATTAAATTAAAAACTTAAT-
1 TAAAACTAAATTAAAAGCTT-ATC
42921 TAAAAC
1 TAAAAC
42927 AAAAAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
23 40 0.91
24 4 0.09
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (23 bp):
TAAAACTAAATTAAAAGCTTATC
Found at i:42942 original size:28 final size:28
Alignment explanation
Indices: 42910--42964 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
42900 AAATTAAATT
42910 AAAAACTTAATTAAAACAAAAAAAATAAC
1 AAAAA-TTAATTAAAACAAAAAAAATAAC
* *
42939 AAAAATTATTTAAAATAAAAAAAATA
1 AAAAATTAATTAAAACAAAAAAAATA
42965 TAAATTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (28 bp):
AAAAATTAATTAAAACAAAAAAAATAAC
Found at i:43610 original size:20 final size:20
Alignment explanation
Indices: 43587--43631 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
43577 AGTTAAATAT
*
43587 ATATTTTTATTAATAATTTA
1 ATATTTTTAATAATAATTTA
* * *
43607 ATATATTTAATATTTATTTA
1 ATATTTTTAATAATAATTTA
43627 ATATT
1 ATATT
43632 AAATATTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTTAATAATAATTTA
Found at i:43616 original size:17 final size:17
Alignment explanation
Indices: 43596--43657 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
43586 TATATTTTTA
43596 TTAATAATTTAATATAT
1 TTAATAATTTAATATAT
*
43613 TTAAT-ATTTATTTAATAT
1 TTAATAATTTA-AT-ATAT
* * *
43631 TAAATATTTTAAAATAT
1 TTAATAATTTAATATAT
43648 TTAA-AATTTA
1 TTAATAATTTA
43658 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
16 10 0.29
17 13 0.37
18 8 0.23
19 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATAATTTAATATAT
Found at i:43636 original size:18 final size:18
Alignment explanation
Indices: 43609--43681 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
43599 ATAATTTAAT
*
43609 ATATTTAATATTTATTTA
1 ATATTAAATATTTATTTA
**
43627 ATATTAAATATTT-TAAA
1 ATATTAAATATTTATTTA
43644 ATATTTAAA-ATTTATTTA
1 ATA-TTAAATATTTATTTA
43662 A-A-TAAATTATTTAATTTA
1 ATATTAAA-TATTT-ATTTA
43680 AT
1 AT
43682 TGATTGAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 4 0.09
17 14 0.32
18 26 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAAATATTTATTTA
Found at i:43636 original size:27 final size:26
Alignment explanation
Indices: 43592--43642 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
43582 AATATATATT
*
43592 TTTATTAATAATTTAATATATTTAATA
1 TTTATTAATAATTAAATAT-TTTAATA
43619 TTTATTTAAT-ATTAAATATTTTAA
1 TTTA-TTAATAATTAAATATTTTAA
43643 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 12 0.55
28 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTATTAATAATTAAATATTTTAATA
Found at i:45723 original size:3 final size:3
Alignment explanation
Indices: 45715--45752 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
45705 GTTTCCCATT
45715 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
45753 TCTGATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48794 original size:90 final size:90
Alignment explanation
Indices: 48641--48822 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 90
48631 TTAGTTATCA
*
48641 AAATGGTATGTTACTTATTCGATTTTTACCCAAACTTCATAGGACACTGTTTTTTTATCTTAATC
1 AAATGGTATGTTACTTATTCGATTTTTACCCAAACTTCATAAGACACTGTTTTTTTATCTTAATC
48706 TTCCAGCCATTTTTGAGAAATAGTG
66 TTCCAGCCATTTTTGAGAAATAGTG
48731 AAATGGTATGTTACTTATTCGATTTTTACCCAAACTTCATAAGACACTGTTTTTTTATCTTAATC
1 AAATGGTATGTTACTTATTCGATTTTTACCCAAACTTCATAAGACACTGTTTTTTTATCTTAATC
48796 TTCCAGCCATTTTTGAGAAATAGTG
66 TTCCAGCCATTTTTGAGAAATAGTG
48821 AA
1 AA
48823 GAAATCTTTA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (90 bp):
AAATGGTATGTTACTTATTCGATTTTTACCCAAACTTCATAAGACACTGTTTTTTTATCTTAATC
TTCCAGCCATTTTTGAGAAATAGTG
Found at i:49622 original size:24 final size:23
Alignment explanation
Indices: 49595--49702 Score: 90
Period size: 24 Copynumber: 4.4 Consensus size: 23
49585 GCTGCATTGC
*
49595 TGGCATTCCTCCTCTGTTGTTTGG
1 TGGCATTCCTCC-CTGTTGTTGGG
**
49619 TGGCATTCCTCCTCCCCAATTGTTGGG
1 TGGCA-T--TCCT-CCCTGTTGTTGGG
* *
49646 TGGCATCCCTCCCTGATTGTTAGG
1 TGGCATTCCTCCCTG-TTGTTGGG
*
49670 TGGCATCCCTCCCATGTTGTTGGG
1 TGGCATTCCTCCC-TGTTGTTGGG
*
49694 AGGCATTCC
1 TGGCATTCC
49703 AGGTGTATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
23 3 0.04
24 42 0.62
25 3 0.04
26 1 0.01
27 17 0.25
28 2 0.03
ACGTcount: A:0.10, C:0.30, G:0.25, T:0.35
Consensus pattern (23 bp):
TGGCATTCCTCCCTGTTGTTGGG
Found at i:52017 original size:23 final size:22
Alignment explanation
Indices: 51975--52017 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
51965 GGCCGGGGTG
51975 GAGAAGAAGGAAGAGAAAGGCC
1 GAGAAGAAGGAAGAGAAAGGCC
* *
51997 GAGAGGAAGGGAAGAGGAAGG
1 GAGAAGAA-GGAAGAGAAAGG
52018 AAGTTAGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.47, C:0.05, G:0.49, T:0.00
Consensus pattern (22 bp):
GAGAAGAAGGAAGAGAAAGGCC
Found at i:52203 original size:17 final size:17
Alignment explanation
Indices: 52176--52227 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
52166 GCAAATTGGC
*
52176 ATTAGTTTAATAATTAAT
1 ATTATTTTAATAA-TAAT
52194 ATT-TTTTAATAATAAT
1 ATTATTTTAATAATAAT
* *
52210 TTTATTTTTATAATAAT
1 ATTATTTTAATAATAAT
52227 A
1 A
52228 AAAATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 6 0.21
17 20 0.69
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTATTTTAATAATAAT
Found at i:52208 original size:20 final size:20
Alignment explanation
Indices: 52183--52228 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
52173 GGCATTAGTT
52183 TAATAATTAATATTTTT-TAA
1 TAATAATT-ATATTTTTATAA
*
52203 TAATAATTTTATTTTTATAA
1 TAATAATTATATTTTTATAA
52223 TAATAA
1 TAATAA
52229 AAATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATAATTATATTTTTATAA
Found at i:52335 original size:20 final size:21
Alignment explanation
Indices: 52310--52355 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
52300 GCATGAGTTT
52310 AATAATTAATATTTAT-TAAA
1 AATAATTAATATTTATATAAA
** *
52330 AATAATTTTTATTTTTATAAA
1 AATAATTAATATTTATATAAA
52351 AATAA
1 AATAA
52356 AAAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAATTAATATTTATATAAA
Found at i:55112 original size:20 final size:20
Alignment explanation
Indices: 55074--55125 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
55064 ATATTATTAT
*
55074 TTAAATGAATTTA-ATAAATA
1 TTAAAT-AATTTATAAAAATA
55094 TTAAATAATTTATAAAAATA
1 TTAAATAATTTATAAAAATA
*
55114 TAAAAT-ATTTAT
1 TTAAATAATTTAT
55126 TTAATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAAATAATTTATAAAAATA
Found at i:57142 original size:50 final size:50
Alignment explanation
Indices: 57080--57178 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
57070 TATTTTGATG
*
57080 GGCTTATTGGATTATGGAATATGTTGATGAGCGTGGGTATTTGGGTTATA
1 GGCTTATTGGATTATGGAATATGTTGATGAGCGTAGGTATTTGGGTTATA
* * * * *
57130 GGCTTGTTGGATTATGGATTATTTTGATGGGCTTAGGTATTTGGGTTAT
1 GGCTTATTGGATTATGGAATATGTTGATGAGCGTAGGTATTTGGGTTAT
57179 GGGTTTTAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.19, C:0.04, G:0.33, T:0.43
Consensus pattern (50 bp):
GGCTTATTGGATTATGGAATATGTTGATGAGCGTAGGTATTTGGGTTATA
Found at i:58248 original size:21 final size:22
Alignment explanation
Indices: 58195--58248 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
58185 GAAAACTTAA
*
58195 AAAAAATGCTTTTCTTAACTTT
1 AAAAAATGTTTTTCTTAACTTT
*
58217 AAAAAGAT-TTTTACTT-A-TTT
1 AAAAA-ATGTTTTTCTTAACTTT
58237 AAAAAATGTTTT
1 AAAAAATGTTTT
58249 ACATAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 12 0.43
21 1 0.04
22 11 0.39
23 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (22 bp):
AAAAAATGTTTTTCTTAACTTT
Found at i:59021 original size:22 final size:22
Alignment explanation
Indices: 58996--59038 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
58986 AAAAGGTCAT
58996 ATAGA-TTAAAAATAAATATTAA
1 ATAGATTTAAAAATAAA-ATTAA
*
59018 ATAGATTTAAAATTAAAATTA
1 ATAGATTTAAAAATAAAATTA
59039 TATATGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
ATAGATTTAAAAATAAAATTAA
Found at i:59170 original size:23 final size:22
Alignment explanation
Indices: 59120--59170 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
59110 TAATTATATT
*
59120 TTTA-TATTATTTTTAATACAA
1 TTTATTATTATTTTAAATACAA
*
59141 TTATATTATTATTTATAAATATAA
1 TT-TATTATTATTT-TAAATACAA
59165 TTTATT
1 TTTATT
59171 GAATATTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 2 0.08
23 12 0.48
24 9 0.36
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTATTATTTTAAATACAA
Found at i:60562 original size:16 final size:15
Alignment explanation
Indices: 60529--60585 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 15
60519 ATAAATTTTG
60529 ATATATTATTATATTTAT
1 ATATATT-TT-TA-TTAT
60547 ATCATATTTTTATTAT
1 AT-ATATTTTTATTAT
60563 -T-TATTTTTATTAT
1 ATATATTTTTATTAT
60576 ATTATATTTT
1 A-TATATTTT
60586 AATTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
13 12 0.34
15 2 0.06
16 10 0.29
17 2 0.06
18 4 0.11
19 5 0.14
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATATTTTTATTAT
Found at i:60567 original size:13 final size:14
Alignment explanation
Indices: 60551--60586 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
60541 ATTTATATCA
60551 TATTTTTATTAT-T
1 TATTTTTATTATAT
60564 TATTTTTATTATAT
1 TATTTTTATTATAT
60578 TATATTTTA
1 TAT-TTTTA
60587 ATTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.57
14 4 0.19
15 5 0.24
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTTTATTATAT
Found at i:63471 original size:13 final size:14
Alignment explanation
Indices: 63443--63469 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
63433 ATTTTTTATT
63443 TTAATACTTAAAAA
1 TTAATACTTAAAAA
63457 TTAATACTTAAAA
1 TTAATACTTAAAA
63470 TTTATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAATACTTAAAAA
Found at i:63609 original size:6 final size:6
Alignment explanation
Indices: 63598--63623 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
63588 ATTTATTATT
63598 AATATA AATATA AATATA AATATA AA
1 AATATA AATATA AATATA AATATA AA
63624 CATTATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:64040 original size:2 final size:2
Alignment explanation
Indices: 64035--64070 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
64025 TACAAGTAAC
64035 AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64071 CTTACATGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:73626 original size:2 final size:2
Alignment explanation
Indices: 73613--73647 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
73603 CTTCATTTAC
* *
73613 GT GT GT GC GT GT GT GT GT GT GT GT GT GT GT CT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
73648 ATGCTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.49, T:0.46
Consensus pattern (2 bp):
GT
Found at i:74742 original size:22 final size:21
Alignment explanation
Indices: 74714--74757 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
74704 TAGGCTTCGA
74714 ATTATGTTAGT-ATGAGGTTAGC
1 ATTATGTTA-TAATGA-GTTAGC
74736 ATTATGTTATAATGAGTTAGC
1 ATTATGTTATAATGAGTTAGC
74757 A
1 A
74758 CTTTTGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.41
Consensus pattern (21 bp):
ATTATGTTATAATGAGTTAGC
Found at i:79945 original size:23 final size:23
Alignment explanation
Indices: 79899--79946 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
79889 CATGTAAAAG
*
79899 TAAAGTTTAATAATTATAAGATT
1 TAAAGTTTAATAATTACAAGATT
* * *
79922 TAAATTTTAATATTTACAATATT
1 TAAAGTTTAATAATTACAAGATT
79945 TA
1 TA
79947 TTTTATTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
TAAAGTTTAATAATTACAAGATT
Found at i:80258 original size:18 final size:18
Alignment explanation
Indices: 80237--80273 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
80227 TTACATTTGA
* *
80237 ACATTTGATTCATTAATT
1 ACATTTGACTCAATAATT
80255 ACATTTGACTCAATAATT
1 ACATTTGACTCAATAATT
80273 A
1 A
80274 ATGAATGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (18 bp):
ACATTTGACTCAATAATT
Done.