Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001058.1 Corchorus capsularis cultivar CVL-1 contig01058, 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: 5936
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--105 Score: 187
Period size: 2 Copynumber: 53.5 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
43 TC TC TC TC TC TC TC TC TC TC TC TC CC TC -C TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
84 TC TC -C TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
106 ATAATGGTTT
Statistics
Matches: 99, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 97 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1456 original size:29 final size:29
Alignment explanation
Indices: 1403--1458 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1393 TTGATGCACA
* *
1403 AATGATCAAAATGCCCTTGTGTGACCCCG
1 AATGACCAAAATGCCCATGTGTGACCCCG
1432 AATGACCAAAATGCCCATG-GATGACCC
1 AATGACCAAAATGCCCATGTG-TGACCC
1459 TAACGCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (29 bp):
AATGACCAAAATGCCCATGTGTGACCCCG
Found at i:4584 original size:7 final size:7
Alignment explanation
Indices: 4564--4730 Score: 67
Period size: 7 Copynumber: 24.1 Consensus size: 7
4554 GTACCAGTCT
4564 TCTTTAC
1 TCTTTAC
**
4571 TGATTAC
1 TCTTTAC
*
4578 TTTTTAC
1 TCTTTAC
4585 TCTTTAC
1 TCTTTAC
*
4592 -CATTT-T
1 TC-TTTAC
4598 TCTTTAC
1 TCTTTAC
**
4605 TGATTAC
1 TCTTTAC
4612 TCTTTAC
1 TCTTTAC
4619 TCTTTAC
1 TCTTTAC
4626 TCTTTAC
1 TCTTTAC
**
4633 -CATTTTT
1 TC-TTTAC
4640 TCTTTAC
1 TCTTTAC
** *
4647 TGATTGC
1 TCTTTAC
4654 -CATTT-C
1 TC-TTTAC
*
4660 -CTTTGC
1 TCTTTAC
**
4666 TGATTAC
1 TCTTTAC
4673 TCTTTAC
1 TCTTTAC
*
4680 TCTTTTC
1 TCTTTAC
4687 TCTTTAC
1 TCTTTAC
* **
4694 TATTTTT
1 TCTTTAC
4701 TCTTTAC
1 TCTTTAC
**
4708 TAATTAC
1 TCTTTAC
4715 TCTTTTAC
1 TC-TTTAC
*
4723 TTTTTAC
1 TCTTTAC
4730 T
1 T
4731 GATTACCATT
Statistics
Matches: 113, Mismatches: 38, Indels: 18
0.67 0.22 0.11
Matches are distributed among these distances:
5 3 0.03
6 8 0.07
7 96 0.85
8 6 0.05
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.58
Consensus pattern (7 bp):
TCTTTAC
Found at i:4591 original size:14 final size:14
Alignment explanation
Indices: 4574--4795 Score: 64
Period size: 14 Copynumber: 15.4 Consensus size: 14
4564 TCTTTACTGA
4574 TTACTTTTTACTCT
1 TTACTTTTTACTCT
*
4588 TTACCATTTT--TCT
1 TTA-CTTTTTACTCT
**
4601 TTACTGATTACTCT
1 TTACTTTTTACTCT
*
4615 TTACTCTTTACTCT
1 TTACTTTTTACTCT
4629 TTACCATTTTT--TCT
1 TTA-C-TTTTTACTCT
*
4643 TTACTGATTGCCATTTC-CT
1 TTACT--TT----TTACTCT
* **
4662 TTGCTGATTACTCT
1 TTACTTTTTACTCT
4676 TTACTCTTTT-CTCT
1 TTACT-TTTTACTCT
*
4690 TTACTATTTT-TTCT
1 TTACT-TTTTACTCT
**
4704 TTACTAATTACTCTT
1 TTACTTTTTACTC-T
**
4719 TTACTTTTTACTGA
1 TTACTTTTTACTCT
*
4733 TTACCATTTTACTCT
1 TTA-CTTTTTACTCT
* ** *
4748 TTTCTAATTACTATT
1 TTACTTTTTACT-CT
**
4763 TTAC-TTTTACTGA
1 TTACTTTTTACTCT
*
4776 TTACCTTTTTACTTT
1 TTA-CTTTTTACTCT
4791 TTACT
1 TTACT
4796 GATTACCATT
Statistics
Matches: 149, Mismatches: 38, Indels: 42
0.65 0.17 0.18
Matches are distributed among these distances:
12 4 0.03
13 15 0.10
14 75 0.50
15 43 0.29
16 4 0.03
18 2 0.01
19 6 0.04
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.58
Consensus pattern (14 bp):
TTACTTTTTACTCT
Found at i:4622 original size:34 final size:34
Alignment explanation
Indices: 4496--4625 Score: 179
Period size: 34 Copynumber: 3.8 Consensus size: 34
4486 GCCATTACTT
* *
4496 TTTACTGATTAGTATTTGACTCTTTACCATTTTTCC
1 TTTACTGATTACTCTTT-ACTCTTTACCATTTTT-C
* * * *
4532 TTTACTGATTACTCTTCACTCTGTACCAGTCTTC
1 TTTACTGATTACTCTTTACTCTTTACCATTTTTC
*
4566 TTTACTGATTACTTTTTACTCTTTACCATTTTTC
1 TTTACTGATTACTCTTTACTCTTTACCATTTTTC
4600 TTTACTGATTACTCTTTACTCTTTAC
1 TTTACTGATTACTCTTTACTCTTTAC
4626 TCTTTACCAT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
34 55 0.67
35 13 0.16
36 14 0.17
ACGTcount: A:0.18, C:0.23, G:0.06, T:0.52
Consensus pattern (34 bp):
TTTACTGATTACTCTTTACTCTTTACCATTTTTC
Found at i:4735 original size:22 final size:21
Alignment explanation
Indices: 4703--4921 Score: 214
Period size: 22 Copynumber: 10.2 Consensus size: 21
4693 CTATTTTTTC
*
4703 TTTACTAATTACTCTTTTACTT
1 TTTACTGATTAC-CTTTTACTT
4725 TTTACTGATTACCATTTTACTCT
1 TTTACTGATTACC-TTTTACT-T
* *
4748 TTT-CTAATTACTATTTTAC-T
1 TTTACTGATTAC-CTTTTACTT
4768 TTTACTGATTACCTTTTTACTT
1 TTTACTGATTACC-TTTTACTT
* *
4790 TTTACTGATTACC-ATTGCTT
1 TTTACTGATTACCTTTTACTT
* *
4810 CTTACTGATTA-CTATTACTT
1 TTTACTGATTACCTTTTACTT
* *
4830 TCTACTGATTACTCTTTTAATT
1 TTTACTGATTAC-CTTTTACTT
4852 TTTACTGATTACCATTTTACTT
1 TTTACTGATTACC-TTTTACTT
* **
4874 TTTACTAATTACCATTTTACCC
1 TTTACTGATTACC-TTTTACTT
4896 TTT-CATGATTACCTTTTACTT
1 TTTAC-TGATTACCTTTTACTT
4917 TTTAC
1 TTTAC
4922 CATTTTACCT
Statistics
Matches: 164, Mismatches: 21, Indels: 24
0.78 0.10 0.11
Matches are distributed among these distances:
19 1 0.01
20 34 0.21
21 25 0.15
22 100 0.61
23 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTACTGATTACCTTTTACTT
Found at i:4987 original size:15 final size:15
Alignment explanation
Indices: 4939--4987 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
4929 CCTTTTTACT
*
4939 CTTAATATCATTTTTA
1 CTTAATACCA-TTTTA
*
4955 C-TAAGTGCCATTTTA
1 CTTAA-TACCATTTTA
4970 CTTAATACCATTTTA
1 CTTAATACCATTTTA
4985 CTT
1 CTT
4988 TCTATCTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 21 0.75
16 7 0.25
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (15 bp):
CTTAATACCATTTTA
Found at i:5428 original size:34 final size:34
Alignment explanation
Indices: 5381--5501 Score: 120
Period size: 34 Copynumber: 3.5 Consensus size: 34
5371 TTAGTTATCA
5381 ATTTACTGATTACTATCTTTTTACATGATTACTG
1 ATTTACTGATTACTATCTTTTTACATGATTACTG
* * * * *
5415 ATTCACTGATTACTAT-TATTTGGACTCTTAATTA-TCA
1 ATTTACTGATTACTATCT-TTT-TA--CATGATTACT-G
*
5452 ATTTACTGATTACTATCTTTTTACCTGATTACTG
1 ATTTACTGATTACTATCTTTTTACATGATTACTG
*
5486 ATTTATTGATTACTAT
1 ATTTACTGATTACTAT
5502 TACCTTGACT
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
33 1 0.01
34 39 0.57
35 2 0.03
36 2 0.03
37 24 0.35
38 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (34 bp):
ATTTACTGATTACTATCTTTTTACATGATTACTG
Found at i:5512 original size:71 final size:71
Alignment explanation
Indices: 5295--5513 Score: 266
Period size: 71 Copynumber: 3.1 Consensus size: 71
5285 GATCATTTTA
* ** * *
5295 ACTCTTAATTATCGATTTACTGATTACTA--TTTTTACCTAGGCT-CTTTAATTACTGATTAATC
1 ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCT-GATTAC-TGATTTACTGATT-A-C
*
5357 TCTTACCTTG
62 TATTACCTTG
* * *
5367 ACTCTTAGTTATCAATTTACTGATTACTATCTTTTTACATGATTACTGATTCACTGATTACTATT
1 ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATT
*
5432 A-TTTGG
66 ACCTT-G
*
5438 ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTATTGATTACTATT
1 ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATT
5503 ACCTTG
66 ACCTTG
5509 ACTCT
1 ACTCT
5514 GATTAATCTC
Statistics
Matches: 127, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
70 2 0.02
71 74 0.58
72 30 0.24
73 12 0.09
74 9 0.07
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (71 bp):
ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATT
ACCTTG
Found at i:5526 original size:55 final size:55
Alignment explanation
Indices: 5479--5779 Score: 494
Period size: 55 Copynumber: 5.5 Consensus size: 55
5469 TTTTTACCTG
* * *
5479 ATTACTGATTTATTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTCACTTA
* *
5534 ATTATTGATTTACTGATTACCATTACCTTGACTCTGATTAATTTCTTTTCACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTCACTTA
* * *
5589 TTTACTGATTTACTGATTACCATTACCTTGACTCTGATTAATCTCTTTTCACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTCACTTA
* *
5644 ATTACTGATTTACTGATTTCTATCACCTTGACTCTGATTAATTTCTTTTCACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTCACTTA
*
5699 ATTACTGATTTACTGATTTCTATTACCTTGACTCTGATTAATTTCTTTTCACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTCACTTA
*
5754 ATTACTGATTTACTGATTTCTATTAC
1 ATTACTGATTTACTGATTACTATTAC
5780 TCTTTACTGA
Statistics
Matches: 232, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 232 1.00
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.50
Consensus pattern (55 bp):
ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTCACTTA
Found at i:5687 original size:25 final size:25
Alignment explanation
Indices: 5659--5744 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 25
5649 TGATTTACTG
5659 ATTTCTATCACCTTGACTCTGATTA
1 ATTTCTATCACCTTGACTCTGATTA
* * *
5684 ATTTCTTTTCA-CTTAATTACTGATTTA
1 ATTTC-TATCACCTTGACT-CTGA-TTA
*
5711 CTGATTTCTATTACCTTGACTCTGATTA
1 ---ATTTCTATCACCTTGACTCTGATTA
5739 ATTTCT
1 ATTTCT
5745 TTTCACTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
25 16 0.34
26 8 0.17
27 3 0.06
28 3 0.06
29 7 0.15
30 10 0.21
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (25 bp):
ATTTCTATCACCTTGACTCTGATTA
Found at i:5804 original size:22 final size:22
Alignment explanation
Indices: 5776--5835 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
5766 CTGATTTCTA
*
5776 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTACCACT
*
5798 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTACCACT
5820 TTAC-CTTTTACTGATT
1 TTACTC-TTTACTGATT
5836 GCATCTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCACT
Done.