Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015808.1 Corchorus capsularis cultivar CVL-1 contig15829, 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: 17393
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:368 original size:6 final size:6
Alignment explanation
Indices: 352--383 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
342 AAAGCAAAGC
352 AAATC- AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
384 GCAAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATCT
Found at i:5570 original size:21 final size:21
Alignment explanation
Indices: 5546--5594 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5536 TCTAACTAAG
*
5546 TCTGATTTGAAT-TTGAAAACC
1 TCTGATTTAAATCTTGAAAA-C
5567 TCTGA-TTAAATCTTGAAAAC
1 TCTGATTTAAATCTTGAAAAC
5587 TCTTGATT
1 TC-TGATT
5595 ACCAATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTGATTTAAATCTTGAAAAC
Found at i:9459 original size:33 final size:33
Alignment explanation
Indices: 9420--9516 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
9410 AGCACTTATG
9420 ACCGGCCACGCGACTTGGAGATGCCC-GCGCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGGC-CAAC
* * * *
9453 ATCGGCCATGCAACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* **
9486 ACCGGCCACGCGACATGGCCATGCCCGGCCA
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCA
9517 CATGACTCGG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 51 0.96
34 2 0.04
ACGTcount: A:0.21, C:0.39, G:0.29, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
Found at i:12507 original size:33 final size:33
Alignment explanation
Indices: 12470--12611 Score: 126
Period size: 33 Copynumber: 4.3 Consensus size: 33
12460 AGCACTTGTG
*
12470 ACCGGCCACACGACTTGGAGATGCCCGCGCAAC-
1 ACCGGCCACACGACTTGGACATGCCCG-GCAACA
** * *
12503 ACCGGCCATGCGACTTGGAGATGCCCGGCCATC-
1 ACCGGCCACACGACTTGGACATGCCCGG-CAACA
* * * * *
12536 ACCGGCCACGCGACATGGCCATGCCCAGCCACA
1 ACCGGCCACACGACTTGGACATGCCCGGCAACA
* * * *
12569 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGCCACACGACTTGGACATGCCCGGCAACA
12602 ACCGGCCACA
1 ACCGGCCACA
12612 TGATCCTTTA
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
32 3 0.03
33 89 0.97
ACGTcount: A:0.23, C:0.42, G:0.26, T:0.09
Consensus pattern (33 bp):
ACCGGCCACACGACTTGGACATGCCCGGCAACA
Found at i:13994 original size:27 final size:26
Alignment explanation
Indices: 13928--13996 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
13918 GTAGATTAAG
*
13928 AATGACCAAAATACCCCTAAATGAAAA
1 AATGACCAAAATGCCCCTAAATG-AAA
13955 AATGACCAAAATGCCCCTGAACATG-AA
1 AATGACCAAAATGCCCCT-AA-ATGAAA
13982 AATGACCAAAATGCC
1 AATGACCAAAATGCC
13997 ATTATGTGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 34 0.87
28 2 0.05
29 3 0.08
ACGTcount: A:0.49, C:0.25, G:0.12, T:0.14
Consensus pattern (26 bp):
AATGACCAAAATGCCCCTAAATGAAA
Found at i:16326 original size:16 final size:15
Alignment explanation
Indices: 16305--16334 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
16295 TTTCAAAATC
16305 ACTTTTTCCAAACCAA
1 ACTTTTT-CAAACCAA
16321 ACTTTTTCAAACCA
1 ACTTTTTCAAACCA
16335 CAACGCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
ACTTTTTCAAACCAA
Done.