Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015925.1 Corchorus capsularis cultivar CVL-1 contig15946, 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: 25896
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--26 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
27 ACTTAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:323 original size:31 final size:31
Alignment explanation
Indices: 252--323 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
242 GTCTATCAAC
252 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
* *
283 TAATT-ATTTGTTTAATTTAATGC-TTCATTT
1 T-TTTAATTTGTTTAATTTAAGGCTTTCATTT
313 GTTTTAATTTG
1 -TTTTAATTTG
324 CAATAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
30 9 0.26
31 24 0.69
32 2 0.06
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTCATTT
Found at i:3204 original size:13 final size:13
Alignment explanation
Indices: 3186--3211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3176 CAAAGTTATT
3186 ACAAAAGTAGGAC
1 ACAAAAGTAGGAC
3199 ACAAAAGTAGGAC
1 ACAAAAGTAGGAC
3212 GTAATAAAAG
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:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (13 bp):
ACAAAAGTAGGAC
Found at i:3990 original size:104 final size:107
Alignment explanation
Indices: 3876--4126 Score: 295
Period size: 104 Copynumber: 2.4 Consensus size: 107
3866 AATTTTTCTA
*
3876 ACCCTTAAAATAAAATTTTAATTTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTT
1 ACCCTTAAAATAAAATTTTAATTTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTT
* * * *
3939 ATTTCT-AAAGCC-TTATAACTATATTATTAATTATGGAATTT
66 ATTTCTAAAACCCATAATAA-TAAATTATTAATTATGAAATTT
* * * * *
3980 ACCCTTAAAATAAAA-ATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTTTGTATTTT
1 ACCCTTAAAATAAAATTTTAATTTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTT
*
4044 ATTTCTAAAACCCAATAATAATAAATTATTAATTTTGAAATTT
66 ATTTCTAAAACCC-ATAATAATAAATTATTAATTATGAAATTT
* * *
4087 ACACTT-AAA-AAAA--TAAAATTTTAATTTGGGGCTAAACTTA
1 ACCCTTAAAATAAAATTTTAATTTTTAATTTGGGGCTAAACTTA
4127 ATAAAAAAGA
Statistics
Matches: 130, Mismatches: 12, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
103 12 0.09
104 57 0.44
105 24 0.18
106 8 0.06
107 24 0.18
108 5 0.04
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (107 bp):
ACCCTTAAAATAAAATTTTAATTTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTT
ATTTCTAAAACCCATAATAATAAATTATTAATTATGAAATTT
Found at i:4644 original size:16 final size:17
Alignment explanation
Indices: 4606--4647 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
4596 TTCTTAAATT
*
4606 TTTTCTTAATTTCACTTTT
1 TTTTCTTAATTT--CTTTC
4625 TTTTCTTAATTT-TTTC
1 TTTTCTTAATTTCTTTC
4641 TTTTCTT
1 TTTTCTT
4648 TTTCCTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 10 0.45
19 12 0.55
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCTTAATTTCTTTC
Found at i:14001 original size:16 final size:16
Alignment explanation
Indices: 13974--14048 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
13964 GTCGGGTTGA
13974 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTCATT
* *
13990 TTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCATT
**
14006 TCGGGTTCGGGTTGTT
1 TCGGGTTCGGGTCATT
* *
14022 T-GGATTCGGGTAATT
1 TCGGGTTCGGGTCATT
14037 TCGGGTTCGGGT
1 TCGGGTTCGGGT
14049 ACCCAAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
15 12 0.25
16 36 0.75
ACGTcount: A:0.07, C:0.12, G:0.40, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGGGTCATT
Found at i:14038 original size:31 final size:31
Alignment explanation
Indices: 13974--14049 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
13964 GTCGGGTTGA
* * *
13974 TCGGGTTCGGGTCATTTTGGGTTTGGGTCATT
1 TCGGGTTCGGGT-ATTTTGGATTCGGGTAATT
14006 TCGGGTTCGGGT-TGTTTGGATTCGGGTAATT
1 TCGGGTTCGGGTAT-TTTGGATTCGGGTAATT
14037 TCGGGTTCGGGTA
1 TCGGGTTCGGGTA
14050 CCCAAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 1 0.03
31 26 0.67
32 12 0.31
ACGTcount: A:0.08, C:0.12, G:0.39, T:0.41
Consensus pattern (31 bp):
TCGGGTTCGGGTATTTTGGATTCGGGTAATT
Found at i:22708 original size:6 final size:6
Alignment explanation
Indices: 22699--22727 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22689 TTTGATTTTT
22699 CTCCAC CTCCAC CTCCAC CTCCAC CTCCA
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCA
22728 GAAGACGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.66, G:0.00, T:0.17
Consensus pattern (6 bp):
CTCCAC
Done.