Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014472.1 Corchorus capsularis cultivar CVL-1 contig14493, 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: 10968
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Found at i:207 original size:26 final size:26
Alignment explanation
Indices: 178--245 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
168 TACTTAATTT
*
178 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
204 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
230 ATTAATTTATGATTAA
1 ATTAGTTTATGATTAA
246 AATGAAGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:289 original size:24 final size:25
Alignment explanation
Indices: 255--313 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
245 AAATGAAGGA
*
255 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
278 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
303 AAATGAAGTTT
1 AAATGAAGTTT
314 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:409 original size:20 final size:20
Alignment explanation
Indices: 384--425 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
374 CAAAAGTGTA
384 AAAAGGGGACGGTATTTAGC
1 AAAAGGGGACGGTATTTAGC
* *
404 AAAAGGGGGCGGTGTTTAGC
1 AAAAGGGGACGGTATTTAGC
424 AA
1 AA
426 TCCAGTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.38, T:0.19
Consensus pattern (20 bp):
AAAAGGGGACGGTATTTAGC
Found at i:695 original size:9 final size:10
Alignment explanation
Indices: 681--738 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 10
671 TCTTTGTTGC
681 TATTATTAT-
1 TATTATTATA
690 TATTATTATA
1 TATTATTATA
700 TATTA-TATA
1 TATTATTATA
709 T-TATATGTATA
1 TAT-TAT-TATA
720 TATTA-TATA
1 TATTATTATA
729 TATATATTAT
1 TAT-TATTAT
739 TAGTAGCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.02
9 23 0.55
10 7 0.17
11 10 0.24
12 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TATTATTATA
Found at i:705 original size:13 final size:14
Alignment explanation
Indices: 681--740 Score: 67
Period size: 13 Copynumber: 4.6 Consensus size: 14
671 TCTTTGTTGC
681 TATTATTAT-TAT-
1 TATTATTATATATA
693 TATTA-TATATTATA
1 TATTATTATA-TATA
*
707 TATTA-TATGTATA
1 TATTATTATATATA
720 TATTA-TATATATA
1 TATTATTATATATA
733 TATTATTA
1 TATTATTA
741 GTAGCTAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
11 3 0.07
12 5 0.12
13 24 0.57
14 10 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TATTATTATATATA
Found at i:708 original size:2 final size:2
Alignment explanation
Indices: 696--735 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
686 TTATTATTAT
*
696 TA TA TA T- TA TA TA T- TA TA TG TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
735 T
1 T
736 TATTAGTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (2 bp):
TA
Found at i:712 original size:20 final size:20
Alignment explanation
Indices: 681--738 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
671 TCTTTGTTGC
681 TATTAT-TATTATTATTATA
1 TATTATATATTATTATTATA
700 TATTATATATTA-TATGTATA
1 TATTATATATTATTAT-TATA
720 TATTATATA-TATATATTAT
1 TATTATATATTAT-TATTAT
739 TAGTAGCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 11 0.31
20 21 0.60
21 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTATATATTATTATTATA
Found at i:3699 original size:19 final size:19
Alignment explanation
Indices: 3655--3701 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
3645 GAGGAGAGAG
* *
3655 TAAGTCATTCTTTTTTCTT
1 TAAGTTATTCTTTTTTCAT
*
3674 TATGTTATTCTTTGTTT-AT
1 TAAGTTATTCTTT-TTTCAT
3693 TAAGTTATT
1 TAAGTTATT
3702 GTAATTGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.64
Consensus pattern (19 bp):
TAAGTTATTCTTTTTTCAT
Found at i:4778 original size:59 final size:61
Alignment explanation
Indices: 4661--4780 Score: 208
Period size: 59 Copynumber: 2.0 Consensus size: 61
4651 TGATATGGAA
4661 GCAAGAGTAGTTGAAACACCAAAGGAGTATGAAAGAGGAAGACTAGCTATCTTTAATCAAAG
1 GCAAGAGTAGTTGAAACACCAAAGGAG-ATGAAAGAGGAAGACTAGCTATCTTTAATCAAAG
*
4723 GCAAGAGTAGTTGAAACACCAGAGGAG-T-AAAGAGGAAGACTAGCTATCTTTAATCAAA
1 GCAAGAGTAGTTGAAACACCAAAGGAGATGAAAGAGGAAGACTAGCTATCTTTAATCAAA
4781 TTTTGATACA
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
59 30 0.53
60 1 0.02
62 26 0.46
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.19
Consensus pattern (61 bp):
GCAAGAGTAGTTGAAACACCAAAGGAGATGAAAGAGGAAGACTAGCTATCTTTAATCAAAG
Found at i:4876 original size:23 final size:23
Alignment explanation
Indices: 4849--4928 Score: 106
Period size: 23 Copynumber: 3.3 Consensus size: 23
4839 GTTTGTGATG
4849 TTTATGTTAGTATTTCTTTCTAT
1 TTTATGTTAGTATTTCTTTCTAT
* *
4872 TTTATGTTGATCTATTACTGTTCTAT
1 TTTATGTT-A-GTATTTCT-TTCTAT
*
4898 TTTATATTAGTATTTCTTTCTAT
1 TTTATGTTAGTATTTCTTTCTAT
4921 TTTATGTT
1 TTTATGTT
4929 TCTTGGGCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
23 21 0.44
24 7 0.15
25 7 0.15
26 13 0.27
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTATGTTAGTATTTCTTTCTAT
Found at i:7195 original size:17 final size:16
Alignment explanation
Indices: 7155--7196 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
7145 CATGTAATCT
*
7155 TTGATCACCGGTGATC
1 TTGATCACAGGTGATC
7171 TTGCATCACAGGTGATC
1 TTG-ATCACAGGTGATC
7188 TTAGATCAC
1 TT-GATCAC
7197 TAGTCATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (16 bp):
TTGATCACAGGTGATC
Found at i:10929 original size:2 final size:2
Alignment explanation
Indices: 10924--10968 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
10914 TATAATGGTG
10924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
10967 TA
1 TA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.