Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011835.1 Corchorus capsularis cultivar CVL-1 contig11856, 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: 16779
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:605 original size:8 final size:9
Alignment explanation
Indices: 566--607 Score: 54
Period size: 8 Copynumber: 4.9 Consensus size: 9
556 AGAAACTATT
566 ATATATAT-
1 ATATATATC
574 ATATATATAC
1 ATATATAT-C
584 ATATATAT-
1 ATATATATC
592 ATATATATC
1 ATATATATC
601 A-ATATAT
1 ATATATAT
608 GTAACTGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 22 0.71
9 1 0.03
10 8 0.26
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATATATC
Found at i:607 original size:2 final size:2
Alignment explanation
Indices: 565--599 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
555 AAGAAACTAT
*
565 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
600 CAATATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4748 original size:13 final size:13
Alignment explanation
Indices: 4730--4755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4720 AACAATTTCC
4730 TGCTAATATAGTG
1 TGCTAATATAGTG
4743 TGCTAATATAGTG
1 TGCTAATATAGTG
4756 ACAAATTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTAATATAGTG
Found at i:7438 original size:21 final size:21
Alignment explanation
Indices: 7395--7438 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7385 GGAAACTGGA
* *
7395 TTGCTAAACACCGCCTCCGTT
1 TTGCTAAACACCGCCCCCCTT
*
7416 TTGCTAAATACCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
7437 TT
1 TT
7439 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.39, G:0.11, T:0.32
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCCTT
Found at i:7558 original size:24 final size:25
Alignment explanation
Indices: 7498--7556 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
7488 TTCAAACCCT
*
7498 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
7523 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
7547 AAA-TTCATTT
1 AAACTTCATTT
7557 TCCTTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:7725 original size:14 final size:14
Alignment explanation
Indices: 7708--7746 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
7698 CAGTTTTTAA
7708 AAAATTAATTTTTT
1 AAAATTAATTTTTT
**
7722 AAAATTTTTTTTTT
1 AAAATTAATTTTTT
7736 AAAATTTAATT
1 AAAA-TTAATT
7747 AGTTTATGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AAAATTAATTTTTT
Found at i:7734 original size:13 final size:14
Alignment explanation
Indices: 7716--7742 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7706 AAAAAATTAA
7716 TTTTTTAAAATTTT
1 TTTTTTAAAATTTT
7730 TTTTTTAAAATTT
1 TTTTTTAAAATTT
7743 AATTAGTTTA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTAAAATTTT
Found at i:7978 original size:20 final size:21
Alignment explanation
Indices: 7952--7996 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
7942 CAAAAATTAT
*
7952 AAAAAGGGGGCGGTATTTAGC
1 AAAAGGGGGGCGGTATTTAGC
*
7973 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGGGCGGTATTTAGC
7994 AAA
1 AAA
7997 CCTCAATGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.40, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGGCGGTATTTAGC
Found at i:9393 original size:6 final size:6
Alignment explanation
Indices: 9384--9408 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9374 TATATACATA
9384 TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT T
9409 TTAAGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Done.