Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006493.1 Corchorus capsularis cultivar CVL-1 contig06514, 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: 17441
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:192 original size:40 final size:40
Alignment explanation
Indices: 77--185 Score: 184
Period size: 40 Copynumber: 2.7 Consensus size: 40
67 CAGTAAAATG
77 GAGTGAAAGTAAAAGAAGTAATCGGTAAAATGGTAATCAA
1 GAGTGAAAGTAAAAGAAGTAATCGGTAAAATGGTAATCAA
117 GAGTGAAAGTAAAAGAAGTAATCGGTAAAATGGTAATCAA
1 GAGTGAAAGTAAAAGAAGTAATCGGTAAAATGGTAATCAA
* *
157 GAGT-AAGAGTAAAGGAAGTAATCAGTAAA
1 GAGTGAA-AGTAAAAGAAGTAATCGGTAAA
186 TCGGTAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 2 0.03
40 64 0.97
ACGTcount: A:0.50, C:0.05, G:0.26, T:0.19
Consensus pattern (40 bp):
GAGTGAAAGTAAAAGAAGTAATCGGTAAAATGGTAATCAA
Found at i:315 original size:26 final size:27
Alignment explanation
Indices: 272--339 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
262 CAAAGAGTAA
* *
272 AATGACAAATGGTGATTAAATTCAA-AG
1 AATGA-AAATAGTAATTAAATTCAAGAG
*
299 AATGAAAATAGTAATTAAGTTCAAGAG
1 AATGAAAATAGTAATTAAATTCAAGAG
**
326 GGTG-AAATAGTAAT
1 AATGAAAATAGTAAT
340 CAGTAAAGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 26 0.74
27 9 0.26
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (27 bp):
AATGAAAATAGTAATTAAATTCAAGAG
Found at i:485 original size:21 final size:21
Alignment explanation
Indices: 446--485 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
436 GGTAAAGAGT
*
446 AAAATGGTAATCAGTAAGGGC
1 AAAATGGTAATCAGCAAGGGC
*
467 AAAATGGTAATTAGCAAGG
1 AAAATGGTAATCAGCAAGG
486 AGTAATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.20
Consensus pattern (21 bp):
AAAATGGTAATCAGCAAGGGC
Found at i:597 original size:17 final size:17
Alignment explanation
Indices: 548--605 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
538 GAAAAAGAAG
*
548 AGTAAAA-ATGGTAATA
1 AGTAAAAGATGGTAATT
*
564 ATTAAGAAGA-GGATAATT
1 AGTAA-AAGATGG-TAATT
582 AGTAAAAGATGGTAATT
1 AGTAAAAGATGGTAATT
*
599 AATAAAA
1 AGTAAAA
606 AGGAGAGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 4 0.12
17 19 0.56
18 11 0.32
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (17 bp):
AGTAAAAGATGGTAATT
Found at i:8179 original size:10 final size:10
Alignment explanation
Indices: 8164--8197 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
8154 CGGTTAAAGC
8164 TCGTTTATGT
1 TCGTTTATGT
8174 TCGTTTATGT
1 TCGTTTATGT
8184 TCGTTTATGT
1 TCGTTTATGT
8194 TCGT
1 TCGT
8198 GAACAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.59
Consensus pattern (10 bp):
TCGTTTATGT
Found at i:16238 original size:34 final size:34
Alignment explanation
Indices: 16199--16272 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
16189 TGAGCAATCT
16199 GCCTGGGCGCCCAGCGGCAGTCGAGCCCTAGCTC
1 GCCTGGGCGCCCAGCGGCAGTCGAGCCCTAGCTC
16233 GCCTGGGCGCCCAGCGGCAGTCGAGCCCTAGCTC
1 GCCTGGGCGCCCAGCGGCAGTCGAGCCCTAGCTC
16267 GCCTGG
1 GCCTGG
16273 TGCTGCGGCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.11, C:0.41, G:0.36, T:0.12
Consensus pattern (34 bp):
GCCTGGGCGCCCAGCGGCAGTCGAGCCCTAGCTC
Done.