Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008899.1 Corchorus capsularis cultivar CVL-1 contig08920, 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: 6449
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:337 original size:146 final size:147
Alignment explanation
Indices: 178--469 Score: 514
Period size: 146 Copynumber: 2.0 Consensus size: 147
168 TGTTGGAATT
178 TTTTTTTGATCATAATAGCTAGCCTAATGGTTTCATATGATCTTTTAAAAAATTTAGATAGCTCT
1 TTTTTTTGATCATAATAGCTAGCCTAATGGTTTCATATGATCTTTTAAAAAATTTAGATAGCTCT
* *
243 AATGTTCTCAAATTTGATTTGGTTTAATTTCATGGCTTTGTTGTTGCTCTTATCAGGGTGGGGTA
66 AATGTTCTCAAATTTGATTTGGTTAAATTTCATGGCTTTGTCGTTGCTCTTATCAGGGTGGGGTA
308 TTTGAATCACAAACCTA
131 TTTGAATCACAAACCTA
* * *
325 TTTTTTT-ATCATAATAGCTAGCCTCATGGTTTCATATGATCTTTTAAAAATTTTAGATAGCTTT
1 TTTTTTTGATCATAATAGCTAGCCTAATGGTTTCATATGATCTTTTAAAAAATTTAGATAGCTCT
*
389 AATGTTCTCAAATTTGATTTGGTTAAATTTCTTGGCTTTGTCGTTGCTCTTATCAGGGTGGGGTA
66 AATGTTCTCAAATTTGATTTGGTTAAATTTCATGGCTTTGTCGTTGCTCTTATCAGGGTGGGGTA
*
454 TTTGAATCTCAAACCT
131 TTTGAATCACAAACCT
470 TACTTTGGGT
Statistics
Matches: 138, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
146 131 0.95
147 7 0.05
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (147 bp):
TTTTTTTGATCATAATAGCTAGCCTAATGGTTTCATATGATCTTTTAAAAAATTTAGATAGCTCT
AATGTTCTCAAATTTGATTTGGTTAAATTTCATGGCTTTGTCGTTGCTCTTATCAGGGTGGGGTA
TTTGAATCACAAACCTA
Found at i:2039 original size:22 final size:21
Alignment explanation
Indices: 2014--2057 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2004 TTATGAACAT
2014 ATAG-CCAATAACCTTTCAATCG
1 ATAGTCCAATAA-C-TTCAATCG
*
2036 ATAGTTCAATAACTTCAATCG
1 ATAGTCCAATAACTTCAATCG
2057 A
1 A
2058 ACACATGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (21 bp):
ATAGTCCAATAACTTCAATCG
Found at i:3015 original size:2 final size:2
Alignment explanation
Indices: 3010--3092 Score: 141
Period size: 2 Copynumber: 42.0 Consensus size: 2
3000 TATATATATA
*
3010 TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
3052 TG T- TG TG TG TG TG TG TG TG TG TG TG GG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3093 AGAACCTGAG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
1 1 0.01
2 75 0.99
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:3385 original size:25 final size:23
Alignment explanation
Indices: 3357--3408 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3347 AATCATTACA
*
3357 AAAATATAATTTTTTAAAAAAATTT
1 AAAATA-AACTTTTT-AAAAAATTT
**
3382 AAAATAAACTTTTTGGAAAATTT
1 AAAATAAACTTTTTAAAAAATTT
3405 AAAA
1 AAAA
3409 CTTAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 7 0.29
25 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAATAAACTTTTTAAAAAATTT
Found at i:5682 original size:26 final size:26
Alignment explanation
Indices: 5626--5682 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5616 TTTCCAATCT
* *
5626 GTTTAGGTAATATTCATTTTGCTGCC
1 GTTTGGGTAATATTCAATTTGCTGCC
* * *
5652 ATTTGGGTGATATTCAATTTGCTTCC
1 GTTTGGGTAATATTCAATTTGCTGCC
5678 GTTTG
1 GTTTG
5683 ATATGTTTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.47
Consensus pattern (26 bp):
GTTTGGGTAATATTCAATTTGCTGCC
Done.