Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013477.1 Corchorus capsularis cultivar CVL-1 contig13498, 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: 6625
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Found at i:250 original size:45 final size:45
Alignment explanation
Indices: 154--281 Score: 145
Period size: 45 Copynumber: 2.8 Consensus size: 45
144 CAAAATTTGT
* * * *
154 AGTTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAG
1 AGTTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAG
* *
199 ATTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 AGTTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAG
*
245 -GTTATCAAAATTTCATAGTG-TGATTATCAAAATTTCA
1 AGTTATCAAAATTTCATAG-GAAGATTATCAAAATTTCA
282 GAATATGATT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
44 14 0.20
45 36 0.51
46 21 0.30
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.37
Consensus pattern (45 bp):
AGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAG
Found at i:440 original size:22 final size:22
Alignment explanation
Indices: 33--526 Score: 193
Period size: 22 Copynumber: 22.6 Consensus size: 22
23 AGTTTAGTTT
33 TCAAAATTTCATAA-GAGGGTTA
1 TCAAAATTTCATAAGGA-GGTTA
* ***
55 TCAAAATTTCAT-AGTATGCAGA
1 TCAAAATTTCATAAGGA-GGTTA
* *
77 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAAGGAGGTTA
* *
99 ACAAAATTTCATAATGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
** * *
121 TCAAAAAATCCTAGGGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
*
143 TCAAAA-TT--T--GTA-GTTA
1 TCAAAATTTCATAAGGAGGTTA
* * *
159 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAAGGAGGTTA
* * *
181 TCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCATAAGGAG-GTTA
* *
204 TCAAAATTTTAT-AGGAAGATTTA
1 TCAAAATTTCATAAGG-AG-GTTA
227 TCAAAATTTCAT-AGCGAGGTTA
1 TCAAAATTTCATAAG-GAGGTTA
* *
249 TCAAAATTTCAT-AGTGTGATTA
1 TCAAAATTTCATAAG-GAGGTTA
* * *
271 TCAAAATTTCAGAA-TATGATTA
1 TCAAAATTTCATAAGGA-GGTTA
*
293 -CTAACAA-TTCATATGGAGGCTT-
1 TC-AA-AATTTCATAAGGAGG-TTA
* * * *
315 TTAAATTTTCATAACGTGGTTA
1 TCAAAATTTCATAAGGAGGTTA
* * *
337 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
* *
359 TCAACATCTCAT-AGTGTTA-GTTA
1 TCAAAATTTCATAAG-G--AGGTTA
**
382 TCAAAATTTCATACTGAGGTCT-
1 TCAAAATTTCATAAGGAGGT-TA
* *
404 TCAAAATTCCTTAAGGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
* * *
426 ACAAAATTTCATAAGAAGCTTA
1 TCAAAATTTCATAAGGAGGTTA
** * ** *
448 AAAAAAATT-ATAAAAAGGTTC
1 TCAAAATTTCATAAGGAGGTTA
* * **
469 TCAAAATTCCAT-AGTATCATTA
1 TCAAAATTTCATAAGGA-GGTTA
* *
491 TTAAAATTTCAT-TGGAAGGTTA
1 TCAAAATTTCATAAGG-AGGTTA
513 TCAAAATTTCATAA
1 TCAAAATTTCATAA
527 TGGGATAAAA
Statistics
Matches: 348, Mismatches: 93, Indels: 61
0.69 0.19 0.12
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
21 27 0.08
22 242 0.70
23 62 0.18
24 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAAGGAGGTTA
Found at i:1632 original size:13 final size:13
Alignment explanation
Indices: 1614--1658 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1604 TAATGCACCC
1614 AAAACATTTAATA
1 AAAACATTTAATA
*
1627 AAAACATTTTAT-
1 AAAACATTTAATA
*
1639 AAATCATTTATATA
1 AAAACATTTA-ATA
1653 AAAACA
1 AAAACA
1659 GTGATAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 8 0.31
13 13 0.50
14 5 0.19
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAACATTTAATA
Found at i:1665 original size:25 final size:25
Alignment explanation
Indices: 1614--1672 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
1604 TAATGCACCC
* *
1614 AAAACATTTAATAAAAACATTTTAT
1 AAAACATTTAATAAAAACATGTGAT
*
1639 AAATCATTTATATAAAAACA-GTGAT
1 AAAACATTTA-ATAAAAACATGTGAT
1664 AAAACATTT
1 AAAACATTT
1673 CCTCAACGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (25 bp):
AAAACATTTAATAAAAACATGTGAT
Found at i:2631 original size:6 final size:6
Alignment explanation
Indices: 2620--2676 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 6
2610 TCCTATTTCC
* * *
2620 CTTTTT CTTTTT C-TTTT C-TTTT C-TTTT CTTTTC CTTTTA CTTTTCC
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT-T
2666 CTTTTT -TTTTT
1 CTTTTT CTTTTT
2677 TGGGCCTTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
5 20 0.44
6 20 0.44
7 5 0.11
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (6 bp):
CTTTTT
Found at i:2636 original size:5 final size:5
Alignment explanation
Indices: 2622--2664 Score: 59
Period size: 5 Copynumber: 8.0 Consensus size: 5
2612 CTATTTCCCT
2622 TTTTC TTTTTC TTTTC TTTTC TTTTC TTTTCC TTTTAC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTT-C TTTT-C TTTTC
2665 CCTTTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 20 0.57
6 15 0.43
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:2673 original size:27 final size:27
Alignment explanation
Indices: 2620--2677 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
2610 TCCTATTTCC
* * *
2620 CTTTTTCTTTTTCTTTTCTTTTCTTTT
1 CTTTTCCTTTTACTTTTCCTTTCTTTT
2647 CTTTTCCTTTTACTTTTCCCTTT-TTTT
1 CTTTTCCTTTTACTTTT-CCTTTCTTTT
2674 -TTTT
1 CTTTT
2678 GGGCCTTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 19 0.70
28 4 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (27 bp):
CTTTTCCTTTTACTTTTCCTTTCTTTT
Done.