Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004807.1 Corchorus capsularis cultivar CVL-1 contig04825, 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: 7241
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:3512 original size:14 final size:14
Alignment explanation
Indices: 3493--3520 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3483 ATGTTTATGC
3493 AAATCCAAATCAAA
1 AAATCCAAATCAAA
3507 AAATCCAAATCAAA
1 AAATCCAAATCAAA
3521 TAAAGAGTGA
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:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATCCAAATCAAA
Found at i:6067 original size:11 final size:11
Alignment explanation
Indices: 6024--6061 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6014 TTCCTATATA
*
6024 AAATAAATTAT
1 AAATTAATTAT
6035 CAAA-TAATTAT
1 -AAATTAATTAT
6046 AAATTAATTAT
1 AAATTAATTAT
6057 AAATT
1 AAATT
6062 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:6303 original size:16 final size:16
Alignment explanation
Indices: 6278--6312 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6268 ATTTTCTTAT
6278 TCTCTATATTCTATTG
1 TCTCTATATTCTATTG
* *
6294 TCTCTCTATTCTTTTG
1 TCTCTATATTCTATTG
6310 TCT
1 TCT
6313 TTTCCATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.06, T:0.60
Consensus pattern (16 bp):
TCTCTATATTCTATTG
Found at i:6404 original size:27 final size:27
Alignment explanation
Indices: 6366--6417 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
6356 TTTCATAACA
6366 AAATTTTATTTCTTAACTGAATTTTCT
1 AAATTTTATTTCTTAACTGAATTTTCT
6393 AAATTTTATTTCTTAACTGAATTTT
1 AAATTTTATTTCTTAACTGAATTTT
6418 TTTAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.56
Consensus pattern (27 bp):
AAATTTTATTTCTTAACTGAATTTTCT
Found at i:6430 original size:27 final size:27
Alignment explanation
Indices: 6373--6430 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
6363 ACAAAATTTT
* *
6373 ATTTCTTAACTGAATTTTCTAAATTTT
1 ATTTCTTAACTGAATTTTCTAAATATA
*
6400 ATTTCTTAACTGAATTTTTTTAAA-ATA
1 ATTTCTTAACTGAA-TTTTCTAAATATA
6427 ATTT
1 ATTT
6431 ATAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (27 bp):
ATTTCTTAACTGAATTTTCTAAATATA
Found at i:6551 original size:13 final size:13
Alignment explanation
Indices: 6528--6583 Score: 98
Period size: 13 Copynumber: 4.5 Consensus size: 13
6518 TTAATATAGG
6528 TATCG-ACGGATA
1 TATCGAACGGATA
6540 TATCGAACGGATA
1 TATCGAACGGATA
6553 TATCGAACGGATA
1 TATCGAACGGATA
6566 TATCG-ACGGATA
1 TATCGAACGGATA
6578 TATCGA
1 TATCGA
6584 GGTATCAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
12 17 0.40
13 25 0.60
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:6574 original size:25 final size:26
Alignment explanation
Indices: 6528--6583 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
6518 TTAATATAGG
6528 TATCG-ACGGATATATCGAACGGATA
1 TATCGAACGGATATATCGAACGGATA
6553 TATCGAACGGATATATCG-ACGGATA
1 TATCGAACGGATATATCGAACGGATA
6578 TATCGA
1 TATCGA
6584 GGTATCAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (26 bp):
TATCGAACGGATATATCGAACGGATA
Done.