Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005226.1 Corchorus capsularis cultivar CVL-1 contig05244, 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: 2433
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Found at i:629 original size:10 final size:10
Alignment explanation
Indices: 614--646 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
604 ACTGGCAATT
614 GGGCGGGTTC
1 GGGCGGGTTC
624 GGGCGGGTTC
1 GGGCGGGTTC
634 GGGCGGGTTC
1 GGGCGGGTTC
644 GGG
1 GGG
647 TACTTCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.64, T:0.18
Consensus pattern (10 bp):
GGGCGGGTTC
Found at i:636 original size:6 final size:6
Alignment explanation
Indices: 617--741 Score: 66
Period size: 6 Copynumber: 20.2 Consensus size: 6
607 GGCAATTGGG
617 CGGGTT CGGG-- CGGGTT CGGG-- CGGGTT CGGGTACTT CGGGTT CGGGTATTTT
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGG---TT CGGGTT CGGG----TT
* * * *
668 CGGGTT TGGGTATTT CGGGTT CGGGCT C-GGAT CGGGTT TGGGTT CGGGTT
1 CGGGTT CGGG---TT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT
718 C-GGTT CCGGG-T CGGGTT CGGGTT C
1 CGGGTT -CGGGTT CGGGTT CGGGTT C
742 ACTTTCGATA
Statistics
Matches: 94, Mismatches: 7, Indels: 36
0.69 0.05 0.26
Matches are distributed among these distances:
4 8 0.09
5 12 0.13
6 55 0.59
7 2 0.02
9 11 0.12
10 6 0.06
ACGTcount: A:0.03, C:0.18, G:0.46, T:0.33
Consensus pattern (6 bp):
CGGGTT
Found at i:671 original size:16 final size:15
Alignment explanation
Indices: 637--692 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
627 CGGGTTCGGG
*
637 CGGGTTCGGGTACTT
1 CGGGTTCGGGTATTT
652 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTA-TTT
*
668 CGGGTTTGGGTATTT
1 CGGGTTCGGGTATTT
683 CGGGTTCGGG
1 CGGGTTCGGG
693 CTCGGATCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 24 0.65
16 13 0.35
ACGTcount: A:0.05, C:0.14, G:0.43, T:0.38
Consensus pattern (15 bp):
CGGGTTCGGGTATTT
Found at i:714 original size:12 final size:11
Alignment explanation
Indices: 684--740 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
674 TGGGTATTTC
*
684 GGGTTCGGGCT
1 GGGTTCGGGTT
* *
695 CGGATCGGGTTT
1 GGGTTCGGG-TT
707 GGGTTCGGGTT
1 GGGTTCGGGTT
* *
718 CGGTTCCGGGTC
1 GGGTT-CGGGTT
730 GGGTTCGGGTT
1 GGGTTCGGGTT
741 CACTTTCGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
11 18 0.51
12 17 0.49
ACGTcount: A:0.02, C:0.18, G:0.49, T:0.32
Consensus pattern (11 bp):
GGGTTCGGGTT
Found at i:739 original size:23 final size:23
Alignment explanation
Indices: 681--741 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
671 GTTTGGGTAT
*
681 TTCGGGTTCGGGCTCGGATCGGG
1 TTCGGGTTCGGGTTCGGATCGGG
* *
704 TTTGGGTTCGGGTTCGGTTCCGGG
1 TTCGGGTTCGGGTTCGGAT-CGGG
728 -TCGGGTTCGGGTTC
1 TTCGGGTTCGGGTTC
742 ACTTTCGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 29 0.88
24 4 0.12
ACGTcount: A:0.02, C:0.20, G:0.46, T:0.33
Consensus pattern (23 bp):
TTCGGGTTCGGGTTCGGATCGGG
Found at i:739 original size:29 final size:29
Alignment explanation
Indices: 681--741 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
671 GTTTGGGTAT
*
681 TTCGGGTTCGGGCTCGGATCGGGTTTGGG
1 TTCGGGTTCGGGCTCGGATCGGGTTCGGG
* *
710 TTCGGGTTC-GGTTCCGGGTCGGGTTCGGG
1 TTCGGGTTCGGGCT-CGGATCGGGTTCGGG
739 TTC
1 TTC
742 ACTTTCGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.02, C:0.20, G:0.46, T:0.33
Consensus pattern (29 bp):
TTCGGGTTCGGGCTCGGATCGGGTTCGGG
Found at i:1509 original size:6 final size:6
Alignment explanation
Indices: 1487--1577 Score: 54
Period size: 6 Copynumber: 15.3 Consensus size: 6
1477 CATTTTGATC
*
1487 TCGGGC TCGGG- TCGGGT TCGGGT TC--GT TCGGGT T---GT CTCGGGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT -TCGGGT
1530 TCGGGTATTT TCGGGT TCGGGT TCGGG- -CGGGTT TCGGGTT TCGGGT
1 TCGGG----T TCGGGT TCGGGT TCGGGT TCGGG-T TCGGG-T TCGGGT
1576 TC
1 TC
1578 ACTTTGCCAG
Statistics
Matches: 71, Mismatches: 0, Indels: 28
0.72 0.00 0.28
Matches are distributed among these distances:
3 2 0.03
4 9 0.13
5 5 0.07
6 36 0.51
7 13 0.18
10 6 0.08
ACGTcount: A:0.01, C:0.19, G:0.45, T:0.35
Consensus pattern (6 bp):
TCGGGT
Found at i:1519 original size:16 final size:16
Alignment explanation
Indices: 1498--1569 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
1488 CGGGCTCGGG
1498 TCGGGTTCGGGTTCGT
1 TCGGGTTCGGGTTCGT
1514 TCGGGTT---G-TC--
1 TCGGGTTCGGGTTCGT
*
1524 TCGGGTTCGGGTAT-TT
1 TCGGGTTCGGGT-TCGT
*
1540 TCGGGTTCGGGTTCGG
1 TCGGGTTCGGGTTCGT
*
1556 GCGGGTTTCGGGTT
1 TCGGG-TTCGGGTT
1570 TCGGGTTCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 17
0.69 0.05 0.27
Matches are distributed among these distances:
10 7 0.16
12 2 0.05
13 2 0.05
15 2 0.05
16 23 0.52
17 8 0.18
ACGTcount: A:0.01, C:0.17, G:0.44, T:0.38
Consensus pattern (16 bp):
TCGGGTTCGGGTTCGT
Found at i:1567 original size:17 final size:17
Alignment explanation
Indices: 1541--1574 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1531 CGGGTATTTT
1541 CGGGTTCGGG-TTCGGG
1 CGGGTTCGGGTTTCGGG
1557 CGGGTTTCGGGTTTCGGG
1 CGGG-TTCGGGTTTCGGG
1575 TTCACTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (17 bp):
CGGGTTCGGGTTTCGGG
Done.