Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013794.1 Corchorus capsularis cultivar CVL-1 contig13815, 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: 2130
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Found at i:73 original size:35 final size:35
Alignment explanation
Indices: 3--170 Score: 155
Period size: 35 Copynumber: 4.8 Consensus size: 35
1 TT
*
3 TTTACTGATTAATTATTTTACTCTTTACCATTTTTTTTC
1 TTTACTGATT-ACTATTTTACTCTTTACCA---TTTTTC
42 TTTACTGATTACT-TTTTACTC-TTACCATTTTTC
1 TTTACTGATTACTATTTTACTCTTTACCATTTTTC
* * * * *
75 TTTACTGATTTCTCTATAACTCTTTACCATTTCTC
1 TTTACTGATTACTATTTTACTCTTTACCATTTTTC
* *
110 TTTACTGATTACT-TTTTACTCTTTACTGA-TTATC
1 TTTACTGATTACTATTTTACTCTTTAC-CATTTTTC
* ** *
144 ATTACTTTTTACCATTTTACTCTTTAC
1 TTTACTGATTACTATTTTACTCTTTAC
171 TGATTGCCTT
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
33 18 0.16
34 30 0.27
35 37 0.33
36 6 0.05
37 8 0.07
38 2 0.02
39 10 0.09
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTACTGATTACTATTTTACTCTTTACCATTTTTC
Found at i:269 original size:26 final size:26
Alignment explanation
Indices: 250--512 Score: 290
Period size: 26 Copynumber: 9.8 Consensus size: 26
240 TACTATTACG
250 CTTTTCTTACTCTTTTTACTGAAT-A-
1 CTTTTCTTACTCTTTTTACTG-ATGAC
*
275 TTGTTTCTTACTCTTTTTACTGATGAC
1 CT-TTTCTTACTCTTTTTACTGATGAC
302 TCTTTTTCTTACTCTTTTTACTGAAT-A-
1 -C-TTTTCTTACTCTTTTTACTG-ATGAC
*
329 CTGTTTCTTACTCTTTTTACTGATGGC
1 CT-TTTCTTACTCTTTTTACTGATGAC
356 TCTTTTCTTACTCTTTTTACTGATGAC
1 -CTTTTCTTACTCTTTTTACTGATGAC
383 TCTTTTTCTTACTCTTTTTACTGAAT-A-
1 -C-TTTTCTTACTCTTTTTACTG-ATGAC
*
410 CTGTTTCTTACTCTTTTTACTGATGGC
1 CT-TTTCTTACTCTTTTTACTGATGAC
437 TCTTTTCTTACTCTTTTTACTGAAT-A-
1 -CTTTTCTTACTCTTTTTACTG-ATGAC
* *
463 TTGTTTCTTACTCTATTTACTGATGACC
1 CT-TTTCTTACTCTTTTTACTGATGA-C
491 CTTTTCTTACTCTTTTTACTGA
1 CTTTTCTTACTCTTTTTACTGA
513 ATATTGTTTT
Statistics
Matches: 207, Mismatches: 10, Indels: 40
0.81 0.04 0.16
Matches are distributed among these distances:
25 12 0.06
26 79 0.38
27 63 0.30
28 48 0.23
29 5 0.02
ACGTcount: A:0.16, C:0.21, G:0.08, T:0.56
Consensus pattern (26 bp):
CTTTTCTTACTCTTTTTACTGATGAC
Found at i:307 original size:53 final size:51
Alignment explanation
Indices: 250--539 Score: 288
Period size: 53 Copynumber: 5.5 Consensus size: 51
240 TACTATTACG
250 CTTTTCTTACTCTTTTTACTGAAT-ATTGTTTCTTACTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTG-ATGATT-TTTCTTACTCTTTTTACTGAT-ACT
* *
303 CTTTTTCTTACTCTTTTTACTGAAT-ACTGTTTCTTACTCTTTTTACTGATGGCT
1 C-TTTTCTTACTCTTTTTACTG-ATGA-TTTTTCTTACTCTTTTTACTGAT-ACT
357 CTTTTCTTACTCTTTTTACTGATGACTCTTTTTCTTACTCTTTTTACTGAATACT
1 CTTTTCTTACTCTTTTTACTGATGA---TTTTTCTTACTCTTTTTACTG-ATACT
* *
412 -GTTTCTTACTCTTTTTACTGATGGCTCTTTTCTTACTCTTTTTACTGAATA-T
1 CTTTTCTTACTCTTTTTACTGAT-GAT-TTTTCTTACTCTTTTTACTG-ATACT
* * *
464 -TGTTTCTTACTCTATTTACTGATGACCCTTTTCTTACTCTTTTTACTGAATATT
1 CT-TTTCTTACTCTTTTTACTGATGA--TTTTTCTTACTCTTTTTACTG-ATACT
*
518 GTTTT-TTA-TCTTTTTTACTGAT
1 CTTTTCTTACTC-TTTTTACTGAT
540 TACTGATTAC
Statistics
Matches: 212, Mismatches: 11, Indels: 28
0.84 0.04 0.11
Matches are distributed among these distances:
52 7 0.03
53 103 0.49
54 74 0.35
55 26 0.12
56 2 0.01
ACGTcount: A:0.16, C:0.19, G:0.08, T:0.57
Consensus pattern (51 bp):
CTTTTCTTACTCTTTTTACTGATGATTTTTCTTACTCTTTTTACTGATACT
Found at i:378 original size:81 final size:81
Alignment explanation
Indices: 252--512 Score: 385
Period size: 81 Copynumber: 3.2 Consensus size: 81
242 CTATTACGCT
*
252 TTTCTTACTCTTTTTACTGAAT--AT-TGTTTCTTACTCTTTTTACTGATGACTCTTTTTCTTAC
1 TTTCTTACTCTTTTTACTG-ATGGCTCT-TTTCTTACTCTTTTTACTGATGACTCTTTTTCTTAC
314 TCTTTTTACTGAATACTG
64 TCTTTTTACTGAATACTG
332 TTTCTTACTCTTTTTACTGATGGCTCTTTTCTTACTCTTTTTACTGATGACTCTTTTTCTTACTC
1 TTTCTTACTCTTTTTACTGATGGCTCTTTTCTTACTCTTTTTACTGATGACTCTTTTTCTTACTC
397 TTTTTACTGAATACTG
66 TTTTTACTGAATACTG
*
413 TTTCTTACTCTTTTTACTGATGGCTCTTTTCTTACTCTTTTTACTGAAT-A-T-TGTTTCTTACT
1 TTTCTTACTCTTTTTACTGATGGCTCTTTTCTTACTCTTTTTACTG-ATGACTCTTTTTCTTACT
*
475 CTATTTACTG-ATGACCCT-
65 CTTTTTACTGAAT-A--CTG
493 TTTCTTACTCTTTTTACTGA
1 TTTCTTACTCTTTTTACTGA
513 ATATTGTTTT
Statistics
Matches: 171, Mismatches: 3, Indels: 14
0.91 0.02 0.07
Matches are distributed among these distances:
78 2 0.01
79 22 0.13
80 40 0.23
81 104 0.61
82 3 0.02
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (81 bp):
TTTCTTACTCTTTTTACTGATGGCTCTTTTCTTACTCTTTTTACTGATGACTCTTTTTCTTACTC
TTTTTACTGAATACTG
Found at i:836 original size:56 final size:56
Alignment explanation
Indices: 532--817 Score: 490
Period size: 56 Copynumber: 5.2 Consensus size: 56
522 TTTATCTTTT
** * *
532 TTACTGA-TTACTGATTACTATTACCTTAACTC-TGATTAATCTC-TTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
*
585 TTACTGATTTACTGATTACTGCTACTTTGAC-CCTGATTAATCTCCTTTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCT-CTTTTTACTTAA
641 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
697 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
753 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
809 TTACTGATT
1 TTACTGATT
818 GCCCCCCTTT
Statistics
Matches: 223, Mismatches: 5, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
53 8 0.04
54 29 0.13
55 1 0.00
56 174 0.78
57 11 0.05
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (56 bp):
TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
Found at i:1580 original size:51 final size:50
Alignment explanation
Indices: 1525--1723 Score: 209
Period size: 51 Copynumber: 3.8 Consensus size: 50
1515 ATGCTAATGC
* * *
1525 TTTATTTACCAATCACTCTAAAGATTCAATCTTTTACCCAAAGACGACATT
1 TTTATTTACCAATTACT-TAAAAATTCAATCTTTTACCCAAAGACGAAATT
* ** * *
1576 TTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGACTAAATC
1 TTTATTTACCAATTACTTAAAAATTC-AATCTTTTACCCAAAGACGAAATT
* * * * *
1627 TTTATTTACTAATTACTCTAAAAATTCAACCTTTTACCCAAAAAAAATGATATT
1 TTTATTTACCAATTACT-TAAAAATTCAATCTTTTACCC---AAAGACGAAATT
*
1681 TTTATTTACCAATTTACTTAAAAATTCAATCTTTTATCCAAAG
1 TTTATTTACCAA-TTACTTAAAAATTCAATCTTTTACCCAAAG
1724 GTTGAATCTT
Statistics
Matches: 120, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
50 7 0.06
51 63 0.52
52 8 0.07
54 37 0.31
55 5 0.04
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (50 bp):
TTTATTTACCAATTACTTAAAAATTCAATCTTTTACCCAAAGACGAAATT
Found at i:1582 original size:105 final size:105
Alignment explanation
Indices: 1470--1704 Score: 266
Period size: 102 Copynumber: 2.2 Consensus size: 105
1460 AAAGGTAACA
* *
1470 TTTTATTTACTAATTACTTAAAAAAAGGTTC-AATCTTTCATTAAAATG-CT-AATGCTTTATTT
1 TTTTATTTACCAATTACTTAAAAAAA--TCCAAATCTTTCATTAAAA-GACTAAAT-CTTTATTT
* * *
1532 ACCAATCACTCTAAAGATTCAATCTTTTACCC-AAAGACGACAT
62 ACCAATCACTCTAAAAATTCAACCTTTTACCCAAAAAACGACAT
* * *
1575 TTTTATTTACCAATTACTT--AAAAATCCAAATCTTTTATTCAAAGACTAAATCTTTATTTACTA
1 TTTTATTTACCAATTACTTAAAAAAATCCAAATCTTTCATTAAAAGACTAAATCTTTATTTACCA
* * *
1638 ATTACTCTAAAAATTCAACCTTTTACCCAAAAAAAATGATAT
66 ATCACTCTAAAAATTCAACCTTTTACCC--AAAAAACGACAT
1680 TTTTATTTACCAATTTACTTAAAAA
1 TTTTATTTACCAA-TTACTTAAAAA
1705 TTCAATCTTT
Statistics
Matches: 110, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
101 3 0.03
102 51 0.46
103 8 0.07
105 39 0.35
106 6 0.05
108 3 0.03
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (105 bp):
TTTTATTTACCAATTACTTAAAAAAATCCAAATCTTTCATTAAAAGACTAAATCTTTATTTACCA
ATCACTCTAAAAATTCAACCTTTTACCCAAAAAACGACAT
Found at i:1646 original size:102 final size:103
Alignment explanation
Indices: 1524--1723 Score: 278
Period size: 102 Copynumber: 1.9 Consensus size: 103
1514 AATGCTAATG
* * *
1524 CTTTATTTACCAATCACTCTAAAGATTCAATCTTTTACCC-AAAGACGACATTTTTATTTACCAA
1 CTTTATTTACCAATCACTCTAAAAATTCAACCTTTTACCCAAAAAACGACATTTTTATTTACCAA
*
1588 -TTACTTAAAAATCCAAATCTTTTATTCAAAGACTAAAT
66 TTTACTTAAAAATCC-AATCTTTTATCCAAAGACTAAAT
* * * *
1626 CTTTATTTACTAATTACTCTAAAAATTCAACCTTTTACCCAAAAAAAATGATATTTTTATTTACC
1 CTTTATTTACCAATCACTCTAAAAATTCAACCTTTTACCC--AAAAAACGACATTTTTATTTACC
*
1691 AATTTACTTAAAAATTCAATCTTTTATCCAAAG
64 AATTTACTTAAAAATCCAATCTTTTATCCAAAG
1724 GTTGAATCTT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
102 36 0.42
105 36 0.42
106 13 0.15
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (103 bp):
CTTTATTTACCAATCACTCTAAAAATTCAACCTTTTACCCAAAAAACGACATTTTTATTTACCAA
TTTACTTAAAAATCCAATCTTTTATCCAAAGACTAAAT
Found at i:1731 original size:20 final size:19
Alignment explanation
Indices: 1708--1762 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1698 TTAAAAATTC
*
1708 AATCTTTTATCCAAAGGTT
1 AATCTTTTAGCCAAAGGTT
*
1727 GAATCTTTAAGCCAAAGGTT
1 -AATCTTTTAGCCAAAGGTT
1747 ATATCTTTTAGCCAAA
1 A-ATCTTTTAGCCAAA
1763 TATCCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (19 bp):
AATCTTTTAGCCAAAGGTT
Done.