Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010181.1 Corchorus capsularis cultivar CVL-1 contig10202, 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: 7204
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:3436 original size:28 final size:28
Alignment explanation
Indices: 3404--3476 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
3394 GTAGATTAAG
*
3404 AATGACCAAAATACCCCCTAAATGCAAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
* **
3432 AATGACCAAAATGCCCCCTAGATGTGAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
3460 AATGACCAAAATGCCCC
1 AATGACCAAAATGCCCC
3477 TGGATGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (28 bp):
AATGACCAAAATGCCCCCTAAATGCAAA
Found at i:4775 original size:22 final size:22
Alignment explanation
Indices: 4746--5329 Score: 179
Period size: 22 Copynumber: 27.1 Consensus size: 22
4736 GCAACCAATA
4746 AAAG-GTAAAATGGTAATCAGT
1 AAAGAGTAAAATGGTAATCAGT
* *
4767 AAAGAGTAAAGTGATAATCAGT
1 AAAGAGTAAAATGGTAATCAGT
* *
4789 AAAGAG--CAATAG-AAGTCAGT
1 AAAGAGTAAAATGGTAA-TCAGT
*
4809 -AAGAAGT--AATAGTACA-CAGT
1 AAAG-AGTAAAATGGTA-ATCAGT
* *
4829 AAAAAAGTAAAAAGGTAATCAGT
1 -AAAGAGTAAAATGGTAATCAGT
* * *
4852 AAAAAGTAAAAAGGT-ATCTG-
1 AAAGAGTAAAATGGTAATCAGT
* * *
4872 AAAGGGTAAAATGGTAATTAAT
1 AAAGAGTAAAATGGTAATCAGT
* *
4894 AAAGAGTAAAGTGATAATCAGT
1 AAAGAGTAAAATGGTAATCAGT
* * *
4916 AAAGAGT--TATAGAAATCAGT
1 AAAGAGTAAAATGGTAATCAGT
* * *
4936 -AAGAAGT--AATAGTAAACAGCA
1 AAAG-AGTAAAATGGTAATCAG-T
* *
4957 AAAAAGTAAAAAGGTAATCAGT
1 AAAGAGTAAAATGGTAATCAGT
* ** *
4979 AAAAAGTAAAAAAGT-ATC-GG
1 AAAGAGTAAAATGGTAATCAGT
* * *
4999 AAAGGGTAAAATGGTAATTAGA
1 AAAGAGTAAAATGGTAATCAGT
* **
5021 AAAGAGTAAACTAATAATCAGT
1 AAAGAGTAAAATGGTAATCAGT
* * *
5043 AAAGACT--AATAGAAATCAGT
1 AAAGAGTAAAATGGTAATCAGT
* *
5063 -AAGAAGTAAGA--GTAAACAGT
1 AAAG-AGTAAAATGGTAATCAGT
* ** *
5083 AAAAAGTAAAAAAGTAATCAAT
1 AAAGAGTAAAATGGTAATCAGT
* * *
5105 AAAAAGTAAAAGGGGT-ATCTGT
1 AAAGAGTAAAA-TGGTAATCAGT
* *
5127 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATGGTAATCAGT
* * *
5149 AAAGAGTAAAGT-G-ATTCGGT
1 AAAGAGTAAAATGGTAATCAGT
*
5169 AAAGAGT--AATAGTAATCAGT
1 AAAGAGTAAAATGGTAATCAGT
* * *
5189 -AAGAAGT--ATTAGTAAACAGT
1 AAAG-AGTAAAATGGTAATCAGT
*
5209 AAA-AGTAAAAAGGGTAATCAGAAAT
1 AAAGAGT-AAAATGGTAATCAG---T
* *
5234 CAAGATTCAAAAAGTAATGGTAATCAGT
1 AAAGAGT----AA--AATGGTAATCAGT
* *
5262 -AAGAGTAAAATAGTAATCAAT
1 AAAGAGTAAAATGGTAATCAGT
* ***
5283 AAAAAAGTAAAAAAATAATCAGT
1 -AAAGAGTAAAATGGTAATCAGT
* *
5306 AAAGAGTAAAATGATAGTCAGT
1 AAAGAGTAAAATGGTAATCAGT
5328 AA
1 AA
5330 TTAAATTCAA
Statistics
Matches: 419, Mismatches: 98, Indels: 91
0.69 0.16 0.15
Matches are distributed among these distances:
18 2 0.00
19 18 0.04
20 117 0.28
21 41 0.10
22 177 0.42
23 39 0.09
25 3 0.01
26 2 0.00
27 5 0.01
28 1 0.00
29 3 0.01
31 11 0.03
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.21
Consensus pattern (22 bp):
AAAGAGTAAAATGGTAATCAGT
Found at i:4897 original size:127 final size:126
Alignment explanation
Indices: 4749--5229 Score: 684
Period size: 127 Copynumber: 3.8 Consensus size: 126
4739 ACCAATAAAA
* * *
4749 GGTAAAATGGTAATCAGTAAAGAGTAAAGTGATAATCAGTAAAGAGCAATAGAAGTCAGTAAGAA
1 GGTAAAATGGTAATTAATAAAGAGTAAAGTGATAATCAGTAAAGAGCAATAGAAATCAGTAAGAA
*
4814 GTAATAGTACACAGTAAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGTATCTGAAAG
66 GTAATAGTAAACAGT-AAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGTATCTGAAAG
**
4876 GGTAAAATGGTAATTAATAAAGAGTAAAGTGATAATCAGTAAAGAGTTATAGAAATCAGTAAGAA
1 GGTAAAATGGTAATTAATAAAGAGTAAAGTGATAATCAGTAAAGAGCAATAGAAATCAGTAAGAA
* * *
4941 GTAATAGTAAACAGCAAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAAAGTATCGGAAAG
66 GTAATAGTAAACAG-TAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGTATCTGAAAG
* *
5003 GGTAAAATGGTAATTAGA-AAAGAGTAAACTAATAATCAGTAAAGA-CTAATAGAAATCAGTAAG
1 GGTAAAATGGTAATTA-ATAAAGAGTAAAGTGATAATCAGTAAAGAGC-AATAGAAATCAGTAAG
* * * *
5066 AAGTAAGAGTAAACAGTAAAAAGTAAAAAAGTAATCAATAAAAAGTAAAAGGGGTATCTGTAAAG
64 AAGTAATAGTAAACAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAA-AGGTATCTG-AAAG
* * * *
5131 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGAT--TCGGTAAAGAGTAATAGTAATCAGTAAGAA
1 GGTAAAATGGTAATTAATAAAGAGTAAAGTGATAATCAGTAAAGAGCAATAGAAATCAGTAAGAA
*
5194 GTATTAGTAAACAGT-AAAAGTAAAAAGGGTAATCAG
66 GTAATAGTAAACAGTAAAAAGTAAAAA-GGTAATCAG
5230 AAATCAAGAT
Statistics
Matches: 316, Mismatches: 30, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
125 11 0.03
126 77 0.24
127 194 0.61
128 34 0.11
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (126 bp):
GGTAAAATGGTAATTAATAAAGAGTAAAGTGATAATCAGTAAAGAGCAATAGAAATCAGTAAGAA
GTAATAGTAAACAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGTATCTGAAAG
Found at i:4947 original size:20 final size:20
Alignment explanation
Indices: 4909--4947 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4899 GTAAAGTGAT
*
4909 AATCAGTAAAGAGTTATAGA
1 AATCAGTAAAGAGTAATAGA
4929 AATCAGT-AAGAAGTAATAG
1 AATCAGTAAAG-AGTAATAG
4948 TAAACAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.23
Consensus pattern (20 bp):
AATCAGTAAAGAGTAATAGA
Found at i:5294 original size:23 final size:22
Alignment explanation
Indices: 5265--5317 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
5255 AATCAGTAAG
*
5265 AGTAAAATAGTAATCAATAAAAA
1 AGTAAAATAATAATCAAT-AAAA
* * *
5288 AGTAAAAAAATAATCAGTAAAG
1 AGTAAAATAATAATCAATAAAA
5310 AGTAAAAT
1 AGTAAAAT
5318 GATAGTCAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.64, C:0.04, G:0.11, T:0.21
Consensus pattern (22 bp):
AGTAAAATAATAATCAATAAAA
Found at i:5398 original size:39 final size:39
Alignment explanation
Indices: 5345--5451 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 39
5335 TTCAAAGAGT
*
5345 AAAATGGTAGTCAGTAAAAGAGAAAAAGAAAAAGAGCAA
1 AAAATGGTAATCAGTAAAAGAGAAAAAGAAAAAGAGCAA
** * ** *
5384 AACGTGGTAATCAGTAAAAAAGAGTAAG-AAAAGAGTAA
1 AAAATGGTAATCAGTAAAAGAGAAAAAGAAAAAGAGCAA
* *
5422 AAAATGGTGATCAGTAAAAAGAGTAAAAGA
1 AAAATGGTAATCAGT-AAAAGAGAAAAAGA
5452 GAGTAATTAG
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
38 21 0.40
39 31 0.60
ACGTcount: A:0.58, C:0.05, G:0.23, T:0.14
Consensus pattern (39 bp):
AAAATGGTAATCAGTAAAAGAGAAAAAGAAAAAGAGCAA
Found at i:5425 original size:10 final size:10
Alignment explanation
Indices: 5396--5425 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
5386 CGTGGTAATC
5396 AGTAAAAAAG
1 AGTAAAAAAG
5406 AGTAAGAAAAG
1 AGTAA-AAAAG
5417 AGTAAAAAA
1 AGTAAAAAA
5426 TGGTGATCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (10 bp):
AGTAAAAAAG
Found at i:5435 original size:38 final size:37
Alignment explanation
Indices: 5338--5457 Score: 113
Period size: 38 Copynumber: 3.2 Consensus size: 37
5328 AATTAAATTC
* **
5338 AAAGAGT--AAAATGGTAGTCAGTAAAAGAGAAAAAGAA
1 AAAGAGTAAAAAATGGTA-TCAGTAAAAAAGAGTAAG-A
* **
5375 AAAGAGCAAAACGTGGTAATCAGTAAAAAAGAGTAAGA
1 AAAGAGTAAAAAATGGT-ATCAGTAAAAAAGAGTAAGA
5413 AAAGAGTAAAAAATGGTGATCAGT-AAAAAGAGTAA-A
1 AAAGAGTAAAAAATGGT-ATCAGTAAAAAAGAGTAAGA
*
5449 AGAGAGTAA
1 AAAGAGTAA
5458 TTAGTAATAA
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
36 9 0.13
37 17 0.25
38 21 0.30
39 21 0.30
40 1 0.01
ACGTcount: A:0.57, C:0.04, G:0.24, T:0.14
Consensus pattern (37 bp):
AAAGAGTAAAAAATGGTATCAGTAAAAAAGAGTAAGA
Found at i:5464 original size:54 final size:55
Alignment explanation
Indices: 5406--5524 Score: 165
Period size: 53 Copynumber: 2.2 Consensus size: 55
5396 AGTAAAAAAG
5406 AGTAAGAAAAGAGTAAAAAATGGTGATCAGT-AAAAAGAGTAAAA-GAGAGTAATT-
1 AGTAAGAAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAATGAG-GT-ATTC
* * *
5460 AGTAA-TAAAGAGTAAGAAATGGTGATCAGTAAAAAAGAGTAAAATGTGGTATTC
1 AGTAAGAAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAATGAGGTATTC
5514 AGTAAGAAAAG
1 AGTAAGAAAAG
5525 GGGTAATTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
53 26 0.46
54 25 0.44
55 6 0.11
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.20
Consensus pattern (55 bp):
AGTAAGAAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAATGAGGTATTC
Found at i:5518 original size:27 final size:26
Alignment explanation
Indices: 5406--5503 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 26
5396 AGTAAAAAAG
5406 AGTAAGAAAAGAGTAAAAAATGGTGATC
1 AGTAA-AAAAGAGT-AAAAATGGTGATC
* *
5434 AGT-AAAAAGAGTAAAAGA-GAGTAATT
1 AGTAAAAAAGAGTAAAA-ATG-GTGATC
*
5460 AGTAATAAAGAGTAAGAAATGGTGATC
1 AGTAAAAAAGAGTAA-AAATGGTGATC
5487 AGTAAAAAAGAGTAAAA
1 AGTAAAAAAGAGTAAAA
5504 TGTGGTATTC
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
25 5 0.08
26 18 0.31
27 30 0.51
28 6 0.10
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.18
Consensus pattern (26 bp):
AGTAAAAAAGAGTAAAAATGGTGATC
Found at i:5562 original size:27 final size:26
Alignment explanation
Indices: 5532--5586 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
5522 AAGGGGTAAT
5532 TAGTAAAAAAAAAGAGTAAAAATATGG
1 TAGTAAAAAAAAAGAGTAAAAA-ATGG
* ** *
5559 TAGTCAGTACAAAGAGTAAAAAATGG
1 TAGTAAAAAAAAAGAGTAAAAAATGG
5585 TA
1 TA
5587 ATTAGTAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (26 bp):
TAGTAAAAAAAAAGAGTAAAAAATGG
Found at i:5600 original size:27 final size:27
Alignment explanation
Indices: 5542--5593 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5532 TAGTAAAAAA
*
5542 AAAGAGTAAAAATATGGTAGTCAGTAC
1 AAAGAGTAAAAATATGGTAATCAGTAC
*
5569 AAAGAGTAAAAA-ATGGTAATTAGTA
1 AAAGAGTAAAAATATGGTAATCAGTA
5594 ATCAAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (27 bp):
AAAGAGTAAAAATATGGTAATCAGTAC
Done.