Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007382.1 Corchorus capsularis cultivar CVL-1 contig07403, 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: 34979
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1728 original size:30 final size:31
Alignment explanation
Indices: 1692--1761 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
1682 GGCGAAAATG
*
1692 CAATTCAGGATACACCGTTAT-GACTTATGT
1 CAATTCAGGATACAACGTTATCGACTTATGT
* ** *
1722 CAATTCAGGATATAACGTTATCGGGTTGTGT
1 CAATTCAGGATACAACGTTATCGACTTATGT
1753 CAATTCAGG
1 CAATTCAGG
1762 CAAATAAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (31 bp):
CAATTCAGGATACAACGTTATCGACTTATGT
Found at i:3085 original size:24 final size:22
Alignment explanation
Indices: 3053--3111 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 22
3043 TTCGGGTGGG
3053 TTTAGATTTTTTTTCAAATAATTTT
1 TTTA-ATTTTTTTTCAAAT-A-TTT
3078 TTTAATTTGTTTTTCAAATATTT
1 TTTAATTT-TTTTTCAAATATTT
3101 TTT-ATTTTTTT
1 TTTAATTTTTTT
3112 AATGCCACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 6 0.18
24 5 0.15
25 14 0.42
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTAATTTTTTTTCAAATATTT
Found at i:3090 original size:25 final size:24
Alignment explanation
Indices: 3053--3103 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
3043 TTCGGGTGGG
3053 TTTAGATTTTTTTTCAAATAATTTT
1 TTTAGATTTTTTTTCAAAT-ATTTT
3078 TTTA-ATTTGTTTTTCAAATATTTT
1 TTTAGATTT-TTTTTCAAATATTTT
3102 TT
1 TT
3104 ATTTTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTAGATTTTTTTTCAAATATTTT
Found at i:5008 original size:16 final size:16
Alignment explanation
Indices: 4987--5017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4977 TTAGTTGAAT
*
4987 TTAGAGTTGGATTTAG
1 TTAGAGTTGAATTTAG
5003 TTAGAGTTGAATTTA
1 TTAGAGTTGAATTTA
5018 TGTACTTGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (16 bp):
TTAGAGTTGAATTTAG
Found at i:15345 original size:32 final size:31
Alignment explanation
Indices: 15309--15371 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
15299 TTGTATATTC
*
15309 AAATGAATTTTAGCTTATCGAA-GTAATATTTT
1 AAATGAATTTTAG-TT-TCGAATGTAAAATTTT
15341 AAATGAATTTTAGTTTCGAATGTAAAATTTT
1 AAATGAATTTTAGTTTCGAATGTAAAATTTT
15372 TTATTTATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 5 0.17
31 11 0.38
32 13 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (31 bp):
AAATGAATTTTAGTTTCGAATGTAAAATTTT
Found at i:19591 original size:2 final size:2
Alignment explanation
Indices: 19584--19621 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
19574 GCACAACACT
*
19584 TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19622 GTTTTTCTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:33472 original size:11 final size:11
Alignment explanation
Indices: 33429--33466 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
33419 TTCCTATATA
*
33429 AAATAAATTAT
1 AAATTAATTAT
33440 CAAA-TAATTAT
1 -AAATTAATTAT
33451 AAATTAATTAT
1 AAATTAATTAT
33462 AAATT
1 AAATT
33467 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:33837 original size:27 final size:27
Alignment explanation
Indices: 33780--33837 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
33770 ACAAAAATTC
* ***
33780 ATTTCTTAACTGAATTTTCTAAATTTC
1 ATTTCTTAACTAAATTTTCTAAATAGA
33807 ATTTCTTAACTAAATTTTCTTAAA-AGA
1 ATTTCTTAACTAAATTTTC-TAAATAGA
33834 ATTT
1 ATTT
33838 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.50
Consensus pattern (27 bp):
ATTTCTTAACTAAATTTTCTAAATAGA
Done.