Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006709.1 Corchorus capsularis cultivar CVL-1 contig06730, 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: 11689
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Found at i:2755 original size:28 final size:28
Alignment explanation
Indices: 2723--2795 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
2713 GTAGATTAAG
2723 AATGACCAAAATACCCCCTAAAAGCAAA
1 AATGACCAAAATACCCCCTAAAAGCAAA
* * * **
2751 AATGACCAAAATGCCCCCTAGATGTGAA
1 AATGACCAAAATACCCCCTAAAAGCAAA
2779 AATGACCAAAATACCCC
1 AATGACCAAAATACCCC
2796 TGGATGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.47, C:0.29, G:0.11, T:0.14
Consensus pattern (28 bp):
AATGACCAAAATACCCCCTAAAAGCAAA
Found at i:3027 original size:28 final size:28
Alignment explanation
Indices: 2995--3067 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
2985 GTAGATTAAG
2995 AATGACCAAAATACCCCCTAAAAGCAAA
1 AATGACCAAAATACCCCCTAAAAGCAAA
* * * **
3023 AATGACCAAAATGCCCCCTAGATGTGAA
1 AATGACCAAAATACCCCCTAAAAGCAAA
3051 AATGACCAAAATACCCC
1 AATGACCAAAATACCCC
3068 TGGATGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.47, C:0.29, G:0.11, T:0.14
Consensus pattern (28 bp):
AATGACCAAAATACCCCCTAAAAGCAAA
Found at i:3038 original size:272 final size:272
Alignment explanation
Indices: 2552--3101 Score: 1091
Period size: 272 Copynumber: 2.0 Consensus size: 272
2542 TCAATGAACT
*
2552 AATTAAGCTTAAACTATATGATTAAAATGCAACAATAGTAAGCTAAATGAAGATGCAACTAAATT
1 AATTAAGCTTAAACTAAATGATTAAAATGCAACAATAGTAAGCTAAATGAAGATGCAACTAAATT
2617 ACTAAATATGCAAAAATGCCAAGGTGCATATTATGATTTTTGGTTTTTCGAATGCAATATAGATA
66 ACTAAATATGCAAAAATGCCAAGGTGCATATTATGATTTTTGGTTTTTCGAATGCAATATAGATA
2682 ACTAAAATGAACAAGCTAATATAAATTAAAAGTAGATTAAGAATGACCAAAATACCCCCTAAAAG
131 ACTAAAATGAACAAGCTAATATAAATTAAAAGTAGATTAAGAATGACCAAAATACCCCCTAAAAG
2747 CAAAAATGACCAAAATGCCCCCTAGATGTGAAAATGACCAAAATACCCCTGGATGACCCTAATGC
196 CAAAAATGACCAAAATGCCCCCTAGATGTGAAAATGACCAAAATACCCCTGGATGACCCTAATGC
2812 TAACTCGACCCA
261 TAACTCGACCCA
2824 AATTAAGCTTAAACTAAATGATTAAAATGCAACAATAGTAAGCTAAATGAAGATGCAACTAAATT
1 AATTAAGCTTAAACTAAATGATTAAAATGCAACAATAGTAAGCTAAATGAAGATGCAACTAAATT
2889 ACTAAATATGCAAAAATGCCAAGGTGCATATTATGATTTTTGGTTTTTCGAATGCAATATAGATA
66 ACTAAATATGCAAAAATGCCAAGGTGCATATTATGATTTTTGGTTTTTCGAATGCAATATAGATA
2954 ACTAAAATGAACAAGCTAATATAAATTAAAAGTAGATTAAGAATGACCAAAATACCCCCTAAAAG
131 ACTAAAATGAACAAGCTAATATAAATTAAAAGTAGATTAAGAATGACCAAAATACCCCCTAAAAG
3019 CAAAAATGACCAAAATGCCCCCTAGATGTGAAAATGACCAAAATACCCCTGGATGACCCTAATGC
196 CAAAAATGACCAAAATGCCCCCTAGATGTGAAAATGACCAAAATACCCCTGGATGACCCTAATGC
3084 TAACTCGACCCA
261 TAACTCGACCCA
3096 AATTAA
1 AATTAA
3102 AGGATATAGG
Statistics
Matches: 277, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
272 277 1.00
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (272 bp):
AATTAAGCTTAAACTAAATGATTAAAATGCAACAATAGTAAGCTAAATGAAGATGCAACTAAATT
ACTAAATATGCAAAAATGCCAAGGTGCATATTATGATTTTTGGTTTTTCGAATGCAATATAGATA
ACTAAAATGAACAAGCTAATATAAATTAAAAGTAGATTAAGAATGACCAAAATACCCCCTAAAAG
CAAAAATGACCAAAATGCCCCCTAGATGTGAAAATGACCAAAATACCCCTGGATGACCCTAATGC
TAACTCGACCCA
Found at i:4181 original size:2 final size:2
Alignment explanation
Indices: 4174--4208 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4164 AGTAAAACCA
4174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4209 CAATAGCTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5813 original size:21 final size:19
Alignment explanation
Indices: 5774--5826 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
5764 AGTAGGATAA
* *
5774 AATTATATTTGTTTTTATATG
1 AATTATATTT-TTTATATA-C
5795 AATTATATTTTTATATATAC
1 AATTATATTTTT-TATATAC
5815 AATTATAATTTT
1 AATTAT-ATTTT
5827 CCATAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTATATTTTTTATATAC
Found at i:9156 original size:6 final size:6
Alignment explanation
Indices: 9137--9173 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
9127 CTATCTATAC
9137 TATCTA TA-CTA TATCTA TATCTA TATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TAT
9174 TAAAAAGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (6 bp):
TATCTA
Found at i:10522 original size:19 final size:20
Alignment explanation
Indices: 10482--10518 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10472 TGTAAGGTGC
*
10482 AATTATTTTATTTGACTTAT
1 AATTAATTTATTTGACTTAT
10502 AATTAATTT-TTTG-CTTA
1 AATTAATTTATTTGACTTA
10519 ATAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 4 0.25
20 8 0.50
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTAATTTATTTGACTTAT
Found at i:11248 original size:18 final size:17
Alignment explanation
Indices: 11216--11249 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11206 TATTTTTCAA
*
11216 TAAAATTTTTGATATAT
1 TAAAATTTTTAATATAT
11233 TAAAATTTTTTAATATA
1 TAAAA-TTTTTAATATA
11250 CAGTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAAATTTTTAATATAT
Done.