Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003087.1 Corchorus capsularis cultivar CVL-1 contig03095, 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, 718
Length: 1198
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.47
Found at i:404 original size:43 final size:42
Alignment explanation
Indices: 344--681 Score: 254
Period size: 43 Copynumber: 7.7 Consensus size: 42
334 CTGATTATTC
*
344 TTTA-TTTTGTACTGATTACTATTCTACTCTTGTTGATTACCT
1 TTTACTTTT-TACTGATTACTATTTTACTCTTGTTGATTACCT
* * *
386 TCTTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTTGT--TGATTAC---CT
* * * *
434 TCTGCTCATTTTTTACTGATTACTCTTTTACT-TTTTACTGATTGCCT
1 T-T--T-ACTTTTTACTGATTACTATTTTACTCTTGT--TGATTACCT
* * * *
481 TTTGCTTTTTAGTGATTACCT-TTTTACTTCTTGCTGATTAGCTT
1 TTTACTTTTTACTGATTA-CTATTTTAC-TCTTGTTGATTA-CCT
* * * ** *
525 TTTACTCTTTACTGATCAC-CTTTTACTCTTACTGATTTCCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* * * **
566 TTTACTTCTTACTTATTACTTTTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* *
607 ATTTACTTTTTACTGACTATTATTTTACTCTTGTTGATTACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
650 TCTTACTTTTTACTGATTACTATTTTACTCTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTT
682 TACTAATTAC
Statistics
Matches: 239, Mismatches: 38, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
41 19 0.08
42 61 0.26
43 84 0.35
44 24 0.10
45 9 0.04
46 1 0.00
47 2 0.01
48 4 0.02
50 13 0.05
51 22 0.09
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
Found at i:417 original size:28 final size:28
Alignment explanation
Indices: 386--465 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 28
376 TTGATTACCT
386 TCTTACTTTTTACTGATTACCATTTTA-
1 TCTTACTTTTTACTGATTACCATTTTAC
*
413 -C-T-C-TTTTACTGATTACTATTTT-C
1 TCTTACTTTTTACTGATTACCATTTTAC
* *
436 TGCTCATTTTTTACTGATTACTC-TTTTAC
1 T-CTTACTTTTTACTGATTAC-CATTTTAC
465 T
1 T
466 TTTTACTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
23 18 0.44
24 1 0.02
25 2 0.05
26 1 0.02
28 17 0.41
29 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.56
Consensus pattern (28 bp):
TCTTACTTTTTACTGATTACCATTTTAC
Found at i:428 original size:15 final size:15
Alignment explanation
Indices: 410--465 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
400 GATTACCATT
410 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
* *
425 TTACTATTTT-CTGC
1 TTACTCTTTTACTGA
* *
439 TCA-TTTTTTACTGA
1 TTACTCTTTTACTGA
453 TTACTCTTTTACT
1 TTACTCTTTTACT
466 TTTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 17 0.53
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:468 original size:21 final size:20
Alignment explanation
Indices: 444--731 Score: 188
Period size: 22 Copynumber: 13.6 Consensus size: 20
434 TCTGCTCATT
444 TTTTACTGATTACTCTTTTAC
1 TTTTACTGATTAC-CTTTTAC
* *
465 TTTTTACTGATTGCCTTTTGC
1 -TTTTACTGATTACCTTTTAC
*
486 TTTTTAGTGATTACCTTTTTAC
1 -TTTTACTGATTACC-TTTTAC
* *
508 TTCTTGCTGATTAGCTTTTTAC
1 TT-TTACTGATTA-CCTTTTAC
*
530 TCTTTACTGATCACCTTTTAC
1 T-TTTACTGATTACCTTTTAC
* *
551 TCTTACTGATTTCCTTTTAC
1 TTTTACTGATTACCTTTTAC
* *
571 TTCTTACTTATTACTTTTTTAC
1 TT-TTACTGATTAC-CTTTTAC
*
593 TCTTACTGATTA-CTATTTAC
1 TTTTACTGATTACCT-TTTAC
* **
613 TTTTTACTGACTATTATTTTAC
1 -TTTTACTGATTA-CCTTTTAC
* **
635 TCTTGTTGATTACCTTCTTAC
1 TTTTACTGATTACCTT-TTAC
*
656 TTTTTACTGATTACTATTTTAC
1 -TTTTACTGATTAC-CTTTTAC
*
678 TCTTTACTAATTACCATTTTACCC
1 T-TTTACTGATTACC-TTTTA--C
702 TTTTA--GA-TACCTTCTTAC
1 TTTTACTGATTACCTT-TTAC
720 TTTTTACTGATT
1 -TTTTACTGATT
732 GCACGCTATT
Statistics
Matches: 207, Mismatches: 37, Indels: 44
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.00
19 8 0.04
20 31 0.15
21 73 0.35
22 83 0.40
23 9 0.04
24 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTTACTGATTACCTTTTAC
Found at i:619 original size:14 final size:13
Alignment explanation
Indices: 545--620 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 13
535 ACTGATCACC
*
545 TTTTACTCTTACT
1 TTTTACTTTTACT
* *
558 GATTTCCTTTTACT
1 -TTTTACTTTTACT
*
572 TCTTACTTATTACTT
1 TTTTACTT-TTAC-T
*
587 TTTTACTCTTACT
1 TTTTACTTTTACT
**
600 GATTACTATTTACT
1 TTTTACT-TTTACT
614 TTTTACT
1 TTTTACT
621 GACTATTATT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
13 11 0.24
14 28 0.61
15 7 0.15
ACGTcount: A:0.18, C:0.20, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTACTTTTACT
Found at i:977 original size:55 final size:55
Alignment explanation
Indices: 916--1194 Score: 434
Period size: 55 Copynumber: 5.1 Consensus size: 55
906 AATTTTAACT
*
916 CTTAATTA-TCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
971 CTTAATTACTGATTTACTGATTACTACTATTTTGACTCTGAATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTG-ATTAATCTCTTTTTA
*
1027 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTATTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
1082 CTTAATTACTGATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * * * *
1137 TTTAATTACTGATTTACTGATTACTGTTACTTTAACTCTGATTTACCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1192 CTT
1 CTT
1195 TTTA
Statistics
Matches: 205, Mismatches: 17, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
55 151 0.74
56 54 0.26
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:1044 original size:111 final size:110
Alignment explanation
Indices: 916--1194 Score: 452
Period size: 111 Copynumber: 2.5 Consensus size: 110
906 AATTTTAACT
*
916 CTTAATTA-TCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTAC
1 CTTAATTACT-GATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAATTAC
**
980 TGATTTACTGATTACTACTATTTTGACTCTGAATTAATCTCTTTTTA
65 TGATTTACTGATTACTACTACCTTGACTCTG-ATTAATCTCTTTTTA
*
1027 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTATTTTTACTTAATTACT
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAATTACT
1092 GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTA
66 GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTA
* * * * *
1137 TTTAATTACTGATTTACTGATTACTGTTACTTTAACTCTGATTTACCTCTTTTTACTT
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTT
1195 TTTA
Statistics
Matches: 157, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
110 67 0.43
111 89 0.57
112 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (110 bp):
CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAATTACT
GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTA
Done.