Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012658.1 Corchorus capsularis cultivar CVL-1 contig12679, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43911
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:588 original size:2 final size:2
Alignment explanation
Indices: 581--605 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
571 AAATAAAATA
581 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 A
606 ACCACGTGAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4087 original size:19 final size:18
Alignment explanation
Indices: 4063--4098 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4053 TGAAGATTTC
4063 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
4082 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
4099 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:5399 original size:15 final size:16
Alignment explanation
Indices: 5379--5412 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5369 GATTGCTCTC
*
5379 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
5394 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
5410 TTA
1 TTA
5413 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:8647 original size:6 final size:6
Alignment explanation
Indices: 8636--8669 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
8626 AAAGCAAAGC
8636 AAATCT AAATCT AAATCT AAATCAT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATC-T AAATCT AAA
8670 ACAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATCT
Found at i:8681 original size:19 final size:19
Alignment explanation
Indices: 8641--8682 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
8631 AAAGCAAATC
* *
8641 TAAATCTAAATCTAAATCA
1 TAAATCTAAAACTAAATAA
8660 TAAATCTAAAAC-AAATTAA
1 TAAATCTAAAACTAAA-TAA
8679 TAAA
1 TAAA
8683 GAAAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAATCTAAAACTAAATAA
Found at i:8682 original size:13 final size:13
Alignment explanation
Indices: 8666--8700 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
8656 ATCATAAATC
8666 TAAAACAAATTAA
1 TAAAACAAATTAA
8679 TAAAGA-AAATTAA
1 TAAA-ACAAATTAA
8692 TAAAACAAA
1 TAAAACAAA
8701 CAATAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (13 bp):
TAAAACAAATTAA
Found at i:14964 original size:6 final size:6
Alignment explanation
Indices: 14953--14986 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
14943 AAAGCAAAGC
*
14953 AAATCT AAATCT AAATCT AAATCTT AAATTT AAA
1 AAATCT AAATCT AAATCT AAATC-T AAATCT AAA
14987 ACAAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATCT
Found at i:14999 original size:13 final size:13
Alignment explanation
Indices: 14983--15017 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
14973 ATCTTAAATT
14983 TAAAACAAATTAA
1 TAAAACAAATTAA
*
14996 TAAAGCAAATTAA
1 TAAAACAAATTAA
15009 TAAAACAAA
1 TAAAACAAA
15018 CAATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.20
Consensus pattern (13 bp):
TAAAACAAATTAA
Found at i:18313 original size:14 final size:14
Alignment explanation
Indices: 18294--18320 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18284 CTCTTACTAA
18294 ACTTAATTACCCTT
1 ACTTAATTACCCTT
18308 ACTTAATTACCCT
1 ACTTAATTACCCT
18321 GAATTAAATT
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:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTTAATTACCCTT
Found at i:18347 original size:35 final size:35
Alignment explanation
Indices: 18308--18677 Score: 623
Period size: 35 Copynumber: 10.6 Consensus size: 35
18298 AATTACCCTT
*
18308 ACTTAATTACCCTGAATTAAATTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
18343 ACTTAATTACCCCGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
18378 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
18413 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
18448 ACTTAATTACCCCGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
18483 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
18518 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
18553 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
18588 ACTTAATTACCCTGAATTAAGTTGATTATTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
18623 ACTTAATTACCCTGAATTAAGTTGATTACTGGCTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
18658 ACTTAATTACCCTGAATTAA
1 ACTTAATTACCCTGAATTAA
18678 ATTACTTATT
Statistics
Matches: 315, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 315 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
Found at i:19481 original size:28 final size:28
Alignment explanation
Indices: 19450--19505 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
19440 CCCGAACCCT
*
19450 TTTTCCTTTT-TTCTTCTTCCTTTTCTTC
1 TTTT-CTTTTCTTCTCCTTCCTTTTCTTC
*
19478 TTTTTTTTTCTTCTCCTTCCTTTTCTTC
1 TTTTCTTTTCTTCTCCTTCCTTTTCTTC
19506 CTCGACGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTTCTTTTCTTCTCCTTCCTTTTCTTC
Found at i:20582 original size:14 final size:14
Alignment explanation
Indices: 20563--20614 Score: 88
Period size: 14 Copynumber: 3.8 Consensus size: 14
20553 GAATCACTTA
20563 TTGCCTTCACTATC
1 TTGCCTTCACTATC
*
20577 TTGCCTTCACT-TA
1 TTGCCTTCACTATC
20590 TTGCCTTCACTATC
1 TTGCCTTCACTATC
20604 TTGCCTTCACT
1 TTGCCTTCACT
20615 TGCATGCTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.34
14 23 0.66
ACGTcount: A:0.13, C:0.35, G:0.08, T:0.44
Consensus pattern (14 bp):
TTGCCTTCACTATC
Found at i:20594 original size:27 final size:27
Alignment explanation
Indices: 20556--20615 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
20546 TTGTGTTGAA
20556 TCACTTATTGCCTTCACTATCTTGCCT
1 TCACTTATTGCCTTCACTATCTTGCCT
20583 TCACTTATTGCCTTCACTATCTTGCCT
1 TCACTTATTGCCTTCACTATCTTGCCT
20610 TCACTT
1 TCACTT
20616 GCATGCTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.45
Consensus pattern (27 bp):
TCACTTATTGCCTTCACTATCTTGCCT
Found at i:20595 original size:13 final size:13
Alignment explanation
Indices: 20556--20615 Score: 84
Period size: 14 Copynumber: 4.5 Consensus size: 13
20546 TTGTGTTGAA
20556 TCACTTATTGCCT
1 TCACTTATTGCCT
*
20569 TCACTATCTTGCCT
1 TCACT-TATTGCCT
20583 TCACTTATTGCCT
1 TCACTTATTGCCT
*
20596 TCACTATCTTGCCT
1 TCACT-TATTGCCT
20610 TCACTT
1 TCACTT
20616 GCATGCTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
13 18 0.43
14 24 0.57
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.45
Consensus pattern (13 bp):
TCACTTATTGCCT
Found at i:27874 original size:24 final size:23
Alignment explanation
Indices: 27847--27893 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
27837 AGTTATTTAG
27847 TTTATGCTT-TATCTTTAATTTTTC
1 TTTAT-CTTATATCTTT-ATTTTTC
*
27871 TTTATCTTATGTCTTTATTTTTC
1 TTTATCTTATATCTTTATTTTTC
27894 AAGTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTATCTTATATCTTTATTTTTC
Found at i:30766 original size:15 final size:16
Alignment explanation
Indices: 30746--30779 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30736 GATTGCTCTC
*
30746 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
30761 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
30777 TTA
1 TTA
30780 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:33933 original size:27 final size:27
Alignment explanation
Indices: 33893--33948 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
33883 TGTGTTATAT
33893 TTTGCTTTTGATTTAGATTTAGATTTAA
1 TTTGCTTTTGATTTAGATTTAG-TTTAA
**
33921 TTTGC-TTTGATTTATTTTTAGTTTAA
1 TTTGCTTTTGATTTAGATTTAGTTTAA
33947 TT
1 TT
33949 GTTTTCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 7 0.27
27 14 0.54
28 5 0.19
ACGTcount: A:0.21, C:0.04, G:0.12, T:0.62
Consensus pattern (27 bp):
TTTGCTTTTGATTTAGATTTAGTTTAA
Found at i:34245 original size:26 final size:27
Alignment explanation
Indices: 34202--34255 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
34192 AATTAATCTG
**
34202 CTCTAAAAAAATTTGTTTTTCCGTTTT
1 CTCTAAAAAAATAAGTTTTTCCGTTTT
*
34229 CTCTAAAAAAA-AAGTTTTTCCTTTTT
1 CTCTAAAAAAATAAGTTTTTCCGTTTT
34255 C
1 C
34256 CGATTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.48
Consensus pattern (27 bp):
CTCTAAAAAAATAAGTTTTTCCGTTTT
Found at i:38472 original size:14 final size:14
Alignment explanation
Indices: 38453--38504 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
38443 ACTGTTTTTT
38453 TCTTTACTGATTAC
1 TCTTTACTGATTAC
**
38467 TCTTTACT-ATTTTTTT
1 TCTTTACTGA---TTAC
38483 TCTTTACTGATTAC
1 TCTTTACTGATTAC
38497 TCTTTACT
1 TCTTTACT
38505 TTTTACTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
16 10 0.33
17 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.04, T:0.60
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:38483 original size:30 final size:29
Alignment explanation
Indices: 38436--38508 Score: 119
Period size: 30 Copynumber: 2.5 Consensus size: 29
38426 ATTTCTTCTC
* *
38436 ACTCCTTACTGTTTTTTTCTTTACTGATT
1 ACTCTTTACTTTTTTTTTCTTTACTGATT
38465 ACTCTTTACTATTTTTTTTCTTTACTGATT
1 ACTCTTTACT-TTTTTTTTCTTTACTGATT
38495 ACTCTTTACTTTTT
1 ACTCTTTACTTTTT
38509 ACTAATTACC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 13 0.32
30 28 0.68
ACGTcount: A:0.15, C:0.19, G:0.04, T:0.62
Consensus pattern (29 bp):
ACTCTTTACTTTTTTTTTCTTTACTGATT
Found at i:38501 original size:44 final size:43
Alignment explanation
Indices: 38453--38749 Score: 230
Period size: 44 Copynumber: 7.2 Consensus size: 43
38443 ACTGTTTTTT
* ** * **
38453 TCTTTACTGATTACTCTTTACTATTTTTTTTCTTTACTGATTAC
1 TCTTTACTGTTTACTAATTACCATTTTACTT-TTTACTGATTAC
*
38497 TCTTTACTTTTTACTAATTACCATTTTACTTTTTACTGATTAC
1 TCTTTACTGTTTACTAATTACCATTTTACTTTTTACTGATTAC
* * * * *
38540 CCTTTTACTCTTTTCTATTTACCATTTTACTTTTCACTGATTAC
1 TC-TTTACTGTTTACTAATTACCATTTTACTTTTTACTGATTAC
* * *
38584 -CTTTACTTTTTACTGATTACCATTTTACTTTTTAGTGATTAC
1 TCTTTACTGTTTACTAATTACCATTTTACTTTTTACTGATTAC
* *
38626 -C--T--T-TTTACTGATTACCA--TTACTTCTTACTGATTAC
1 TCTTTACTGTTTACTAATTACCATTTTACTTTTTACTGATTAC
* * *
38661 T-ATTACTTTTTACTGATTACCATTTT--TTCTTTACTGATTAC
1 TCTTTACTGTTTACTAATTACCATTTTACTT-TTTACTGATTAC
* * **
38702 TTTTTAC--TTCACTCTTTACCATTTT-CTTTTTACTGATCT-C
1 TCTTTACTGTTTACTAATTACCATTTTACTTTTTACTGAT-TAC
38742 TCTTTACT
1 TCTTTACT
38750 TTACTCTTTA
Statistics
Matches: 213, Mismatches: 26, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
35 16 0.08
37 15 0.07
38 1 0.00
39 1 0.00
40 48 0.23
41 15 0.07
42 42 0.20
43 14 0.07
44 61 0.29
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.56
Consensus pattern (43 bp):
TCTTTACTGTTTACTAATTACCATTTTACTTTTTACTGATTAC
Found at i:38527 original size:22 final size:22
Alignment explanation
Indices: 38485--38634 Score: 186
Period size: 22 Copynumber: 7.0 Consensus size: 22
38475 ATTTTTTTTC
38485 TTTACTGATTA-C-TCTTTACTT
1 TTTACTGATTACCAT-TTTACTT
*
38506 TTTACTAATTACCATTTTACTT
1 TTTACTGATTACCATTTTACTT
*
38528 TTTACTGATTACCCTTTTACTCT
1 TTTACTGATTACCATTTTACT-T
38551 TTT-CT-ATTTACCATTTTACTT
1 TTTACTGA-TTACCATTTTACTT
*
38572 TTCACTGATTACC--TTTACTT
1 TTTACTGATTACCATTTTACTT
38592 TTTACTGATTACCATTTTACTT
1 TTTACTGATTACCATTTTACTT
* *
38614 TTTAGTGATTACCTTTTTACT
1 TTTACTGATTACCATTTTACT
38635 GATTACCATT
Statistics
Matches: 113, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
20 19 0.17
21 14 0.12
22 74 0.65
23 6 0.05
ACGTcount: A:0.21, C:0.20, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACTT
Found at i:38629 original size:15 final size:15
Alignment explanation
Indices: 38611--38687 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 15
38601 TACCATTTTA
*
38611 CTTTTTAGTGATTAC
1 CTTTTTACTGATTAC
38626 CTTTTTACTGATTAC
1 CTTTTTACTGATTAC
* **
38641 C--ATTACTTCTTA-
1 CTTTTTACTGATTAC
**
38653 CTGATTACT-ATTA-
1 CTTTTTACTGATTAC
38666 CTTTTTACTGATTAC
1 CTTTTTACTGATTAC
38681 CATTTTT
1 C-TTTTT
38688 TCTTTACTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
12 1 0.02
13 18 0.36
14 10 0.20
15 16 0.32
16 5 0.10
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.53
Consensus pattern (15 bp):
CTTTTTACTGATTAC
Found at i:38636 original size:57 final size:55
Alignment explanation
Indices: 38569--38687 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 55
38559 TACCATTTTA
* * * * *
38569 CTTTTCACTGATTACCTTTACTTTTTACTGATTACCATTTTACTTTTTAGTGATTAC
1 CTTTTTACTGATTACCATTACTTCTTACTGATTA-C-TATTACTTTTTACTGATTAC
38626 CTTTTTACTGATTACCATTACTTCTTACTGATTACTATTACTTTTTACTGATTAC
1 CTTTTTACTGATTACCATTACTTCTTACTGATTACTATTACTTTTTACTGATTAC
38681 CATTTTT
1 C-TTTTT
38688 TCTTTACTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
55 19 0.34
56 6 0.11
57 31 0.55
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (55 bp):
CTTTTTACTGATTACCATTACTTCTTACTGATTACTATTACTTTTTACTGATTAC
Found at i:38667 original size:77 final size:75
Alignment explanation
Indices: 38566--38709 Score: 213
Period size: 77 Copynumber: 1.9 Consensus size: 75
38556 ATTTACCATT
*
38566 TTACTTTTCACTGATTACCTTTACTTTTTACTGATTACCATTTTACTT-TTTAGTGATTACCTTT
1 TTACTTTTCACTGATTACCTTTACTTTTTACTGATTACCATTTT--TTCTTTACTGATTA-CTTT
38630 TTACTGATTACCA
63 TTACTGATTACCA
38643 TTACTTCTT-ACTGATTA-CTATTACTTTTTACTGATTACCATTTTTTCTTTACTGATTACTTTT
1 TTACTT-TTCACTGATTACCT-TTACTTTTTACTGATTACCATTTTTTCTTTACTGATTACTTTT
38706 TACT
64 TACT
38710 TCACTCTTTA
Statistics
Matches: 63, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
75 11 0.17
76 12 0.19
77 38 0.60
78 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.54
Consensus pattern (75 bp):
TTACTTTTCACTGATTACCTTTACTTTTTACTGATTACCATTTTTTCTTTACTGATTACTTTTTA
CTGATTACCA
Found at i:38721 original size:40 final size:39
Alignment explanation
Indices: 38478--38860 Score: 140
Period size: 40 Copynumber: 9.7 Consensus size: 39
38468 CTTTACTATT
* **
38478 TTTTTTCTTTACTGATTACTCTTTACTTTTTACTAATTACCA
1 TTTTTTCTTTACTGATTACT-TTTAC--TTCACTCTTTACCA
** *
38520 TTTTACTT-TTTACTGATTACCCTTTTACTCTTTTCTATTTACCA
1 TTTT--TTCTTTACTGATTA--CTTTTA--CTTCACTCTTTACCA
* * * **
38564 TTTTACTT-TTCACTGATTACCTTTACTTTTTACTGATTACCA
1 TTTT--TTCTTTACTGATTACTTTTAC--TTCACTCTTTACCA
* * **
38606 TTTTACTT-TTTAGTGATTACCTTT--TT-ACTGATTACCA
1 TTTT--TTCTTTACTGATTACTTTTACTTCACTCTTTACCA
** * * **
38643 TTACTTC-TTACTGATTACTATTACTTTTTACTGATTACCA
1 TTTTTTCTTTACTGATTACTTTTAC--TTCACTCTTTACCA
38683 TTTTTTCTTTACTGATTACTTTTTACTTCACTCTTTACCA
1 TTTTTTCTTTACTGATTAC-TTTTACTTCACTCTTTACCA
*
38723 TTTTCTT-TTTACTGATCT-CTCTTTACTTTACTCTTTA-C-
1 TTTT-TTCTTTACTGAT-TACT-TTTACTTCACTCTTTACCA
** * *
38761 TCTTTACCATTTTACTAATTAC---T-CTTCATTCTTTACCA
1 T-TTTTTC--TTTACTGATTACTTTTACTTCACTCTTTACCA
*
38799 TTTTTTTCTTTACTGATTAC---T-CTTTACTCTTTACCA
1 -TTTTTTCTTTACTGATTACTTTTACTTCACTCTTTACCA
*
38835 -TTTTTCTTCACTGATTACTCTTTACT
1 TTTTTTCTTTACTGATTACT-TTTACT
38861 GATTGCCTTT
Statistics
Matches: 277, Mismatches: 32, Indels: 67
0.74 0.09 0.18
Matches are distributed among these distances:
34 17 0.06
35 14 0.05
36 35 0.13
37 15 0.05
38 8 0.03
39 10 0.04
40 58 0.21
41 23 0.08
42 47 0.17
43 11 0.04
44 36 0.13
45 2 0.01
46 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (39 bp):
TTTTTTCTTTACTGATTACTTTTACTTCACTCTTTACCA
Found at i:38811 original size:36 final size:34
Alignment explanation
Indices: 38742--38856 Score: 118
Period size: 36 Copynumber: 3.5 Consensus size: 34
38732 TACTGATCTC
*
38742 TCTTTACT--TTACTCTTTACTCTTTACCA----
1 TCTTTACTGATTACTCTTCACTCTTTACCATTTT
* *
38770 T-TTTACTAATTACTCTTCATTCTTTACCATTTTTT
1 TCTTTACTGATTACTCTTCACTCTTTACCA--TTTT
*
38805 TCTTTACTGATTACTCTTTACTCTTTACCATTTT
1 TCTTTACTGATTACTCTTCACTCTTTACCATTTT
*
38839 TCTTCACTGATTACTCTT
1 TCTTTACTGATTACTCTT
38857 TACTGATTGC
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
27 6 0.08
28 1 0.01
29 18 0.25
34 21 0.29
35 1 0.01
36 25 0.35
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.56
Consensus pattern (34 bp):
TCTTTACTGATTACTCTTCACTCTTTACCATTTT
Found at i:38969 original size:26 final size:26
Alignment explanation
Indices: 38940--39068 Score: 129
Period size: 26 Copynumber: 4.9 Consensus size: 26
38930 CTATTGCGCT
*
38940 TTTCTTACTCTCTTTACTGAATATTC
1 TTTCTTACTCTTTTTACTGAATATTC
* *
38966 TTTCCTACTCTTTTTACTG-ATGACTTT
1 TTTCTTACTCTTTTTACTGAAT-A-TTC
* * *
38993 TTTC-TACTCTTCTTACTGAATACTG
1 TTTCTTACTCTTTTTACTGAATATTC
**
39018 TTTCTTACTCTTTTTACTG-ATGGCTC
1 TTTCTTACTCTTTTTACTGAAT-ATTC
39044 TTTTCTTACTCTTTTTACTGAATAT
1 -TTTCTTACTCTTTTTACTGAATAT
39069 CCCATAAAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
25 9 0.11
26 47 0.55
27 27 0.32
28 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.07, T:0.54
Consensus pattern (26 bp):
TTTCTTACTCTTTTTACTGAATATTC
Found at i:39011 original size:52 final size:53
Alignment explanation
Indices: 38938--39068 Score: 185
Period size: 52 Copynumber: 2.5 Consensus size: 53
38928 TACTATTGCG
38938 CTTTTCTTACTC-TCTTTACTGAATATTCTTTCCTACTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTC-TTACTGAATATTCTTTCCTACTCTTTTTACTGATGACT
* * * * *
38991 TTTTTC-TACTCTTCTTACTGAATACTGTTTCTTACTCTTTTTACTGATGGCT
1 CTTTTCTTACTCTTCTTACTGAATATTCTTTCCTACTCTTTTTACTGATGACT
*
39043 CTTTTCTTACTCTTTTTACTGAATAT
1 CTTTTCTTACTCTTCTTACTGAATAT
39069 CCCATAAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
52 44 0.65
53 24 0.35
ACGTcount: A:0.17, C:0.22, G:0.07, T:0.54
Consensus pattern (53 bp):
CTTTTCTTACTCTTCTTACTGAATATTCTTTCCTACTCTTTTTACTGATGACT
Found at i:39231 original size:15 final size:16
Alignment explanation
Indices: 39199--39232 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39189 AAAGAAGAAT
*
39199 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
39215 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
39230 TAA
1 TAA
39233 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:40551 original size:19 final size:18
Alignment explanation
Indices: 40518--40553 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40508 TTGAAATAAC
40518 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
40536 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
40554 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.