Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002138.1 Corchorus capsularis cultivar CVL-1 contig02142, 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, 738
Length: 1231
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Found at i:548 original size:6 final size:6
Alignment explanation
Indices: 537--599 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
527 GGGATCACTA
* *
537 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
581 ACTAAT TCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A
600 GAATAGAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
5 19 0.38
6 31 0.62
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33
Consensus pattern (6 bp):
ACTAAT
Found at i:554 original size:11 final size:11
Alignment explanation
Indices: 533--598 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 11
523 AGCCGGGATC
533 ACTAA-CTAAT
1 ACTAATCTAAT
543 ACTAATCTAAT
1 ACTAATCTAAT
*
554 ACTAATAGAATAGAAT
1 ACTAAT---CT--AAT
570 ACTAATCTAAT
1 ACTAATCTAAT
581 ACTAATTCTAAT
1 ACTAA-TCTAAT
593 ACTAAT
1 ACTAAT
599 AGAATAGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 5 0.11
11 20 0.43
12 11 0.23
13 1 0.02
14 1 0.02
16 9 0.19
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.33
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:597 original size:39 final size:37
Alignment explanation
Indices: 533--607 Score: 132
Period size: 39 Copynumber: 2.0 Consensus size: 37
523 AGCCGGGATC
533 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT
1 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT
570 ACTAATCTAATACTAATTCTAATACTAATAGAATAGAA
1 ACTAA-CTAATACTAA-TCTAATACTAATAGAATAGAA
608 AAAATAGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 5 0.14
38 10 0.28
39 21 0.58
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (37 bp):
ACTAACTAATACTAATCTAATACTAATAGAATAGAAT
Found at i:615 original size:14 final size:14
Alignment explanation
Indices: 596--623 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
586 TTCTAATACT
596 AATAGAATAGAAAA
1 AATAGAATAGAAAA
610 AATAGAATAGAAAA
1 AATAGAATAGAAAA
624 TACTAATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:633 original size:18 final size:18
Alignment explanation
Indices: 590--640 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
580 TACTAATTCT
590 AATACTAATAGAATAG-A
1 AATACTAATAGAATAGAA
607 AA-A--AATAGAATAGAA
1 AATACTAATAGAATAGAA
622 AATACTAATAGAATAGAA
1 AATACTAATAGAATAGAA
640 A
1 A
641 GAAAAGAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.33
15 3 0.10
16 2 0.07
17 2 0.07
18 13 0.43
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.20
Consensus pattern (18 bp):
AATACTAATAGAATAGAA
Found at i:1200 original size:15 final size:14
Alignment explanation
Indices: 1170--1196 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1160 GAAGGGAATA
1170 AAATAAAAAAAAAG
1 AAATAAAAAAAAAG
1184 AAATAAAAAAAAA
1 AAATAAAAAAAAA
1197 AGAAGGGGGA
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:0.89, C:0.00, G:0.04, T:0.07
Consensus pattern (14 bp):
AAATAAAAAAAAAG
Done.