Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006697.1 Corchorus capsularis cultivar CVL-1 contig06718, 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: 16220
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:385 original size:59 final size:57
Alignment explanation
Indices: 236--395 Score: 234
Period size: 59 Copynumber: 2.8 Consensus size: 57
226 CAACTAATTC
* * **
236 TCTT-TTTGTTTC-TAATTGACTCAATTACCCTGAATTAAGCGTTTATTACTGACTA
1 TCTTCTTTGATTCTTAACTGACTCAATTACCCTGAATTAAGCCATTATTACTGACTA
*
291 TCTTCTTTGATTCTTAACTGACTCAATTACCCTGAATTAAGCCATTATTACTGATTA
1 TCTTCTTTGATTCTTAACTGACTCAATTACCCTGAATTAAGCCATTATTACTGACTA
*
348 TCTTTTCTTTGATTCTTAACTGACTCAATTACCCTGAATTAAACCATT
1 TC--TTCTTTGATTCTTAACTGACTCAATTACCCTGAATTAAGCCATT
396 TTATTTTCTC
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
55 4 0.04
56 7 0.07
57 41 0.43
59 43 0.45
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.44
Consensus pattern (57 bp):
TCTTCTTTGATTCTTAACTGACTCAATTACCCTGAATTAAGCCATTATTACTGACTA
Found at i:486 original size:35 final size:36
Alignment explanation
Indices: 447--777 Score: 355
Period size: 36 Copynumber: 9.2 Consensus size: 36
437 CTAAACTAAC
447 TTACTTATTGAACT-ACTTAATTACCCTGAATTAAG
1 TTACTTATTGAACTCACTTAATTACCCTGAATTAAG
* *
482 TTACTCATT-AACTCACTTAACTACCCTGAATTAAG
1 TTACTTATTGAACTCACTTAATTACCCTGAATTAAG
*
517 TTACTTATT-AAATCACTTAATTACCCTGAATTGAAG
1 TTACTTATTGAACTCACTTAATTACCCTGAATT-AAG
*
553 TTGA-TTACTG-ACTCACTTAATTACCCTGAATTAAG
1 TT-ACTTATTGAACTCACTTAATTACCCTGAATTAAG
* *
588 TTACTCATTGAACT-ACTTAATTATCCTGAATTAAG
1 TTACTTATTGAACTCACTTAATTACCCTGAATTAAG
* *
623 TTACTTATT-AACTCACTTAATTTCCCCGAATTAAAG
1 TTACTTATTGAACTCACTTAATTACCCTGAATT-AAG
*
659 TTGA-TTACTG-ACTCACTTAATTACCCTGAATTAAAG
1 TT-ACTTATTGAACTCACTTAATTACCCTGAATT-AAG
*
695 TTGA-TTACTG-ACTCACTTAATTACCCTGAATTAAAG
1 TT-ACTTATTGAACTCACTTAATTACCCTGAATT-AAG
**
731 TTGA-TTATT-ACCGACTTGCTTAATTACCCTGAATTAAG
1 TT-ACTTATTGA---ACTCACTTAATTACCCTGAATTAAG
*
769 TTGCTTATT
1 TTACTTATT
778 ACTGACTCAC
Statistics
Matches: 260, Mismatches: 21, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
34 9 0.03
35 109 0.42
36 110 0.42
37 2 0.01
38 10 0.04
39 20 0.08
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (36 bp):
TTACTTATTGAACTCACTTAATTACCCTGAATTAAG
Found at i:654 original size:106 final size:107
Alignment explanation
Indices: 461--728 Score: 418
Period size: 106 Copynumber: 2.5 Consensus size: 107
451 TTATTGAACT
*
461 ACTTAATTACCCTGAATTAAGTTACTCATT-AACTCACTTAACTACCCTGAATTAAGTTACTTAT
1 ACTTAATTACCCTGAATTAAGTTACTCATTGAACTCACTTAATTACCCTGAATTAAGTTACTTAT
* *
525 TAAATCACTTAATTACCCTGAATTGAAGTTGATTACTGACTC
66 TAAATCACTTAATTACCCCGAATTAAAGTTGATTACTGACTC
*
567 ACTTAATTACCCTGAATTAAGTTACTCATTGAACT-ACTTAATTATCCTGAATTAAGTTACTTAT
1 ACTTAATTACCCTGAATTAAGTTACTCATTGAACTCACTTAATTACCCTGAATTAAGTTACTTAT
* *
631 TAACTCACTTAATTTCCCCGAATTAAAGTTGATTACTGACTC
66 TAAATCACTTAATTACCCCGAATTAAAGTTGATTACTGACTC
* *
673 ACTTAATTACCCTGAATTAAAGTTGA-TTACTG-ACTCACTTAATTACCCTGAATTAA
1 ACTTAATTACCCTGAATT-AAGTT-ACTCATTGAACTCACTTAATTACCCTGAATTAA
729 AGTTGATTAT
Statistics
Matches: 149, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
106 116 0.78
107 32 0.21
108 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (107 bp):
ACTTAATTACCCTGAATTAAGTTACTCATTGAACTCACTTAATTACCCTGAATTAAGTTACTTAT
TAAATCACTTAATTACCCCGAATTAAAGTTGATTACTGACTC
Found at i:5481 original size:48 final size:47
Alignment explanation
Indices: 5406--5737 Score: 405
Period size: 48 Copynumber: 6.9 Consensus size: 47
5396 ATTTTTAATC
* *
5406 TTTACTTGCTTCTTCCTAAAACGCCCTTCCCAGACGGAAGGCACTTAT
1 TTTACTTGCTT-TTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* * * *
5454 TTTACTTGCTTCTTCCCAAAACACCCTTCCCAGATGGAAGACACTTAT
1 TTTACTTGCTT-TTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
*
5502 TTTACTTGCTGTTTCCCAAAACGCCCTTCTCGGACGGAAGGCACTTAT
1 TTTACTTGCT-TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* * *
5550 TTTACTTGCTTCTTCCCAAGATGCCCTTCCCAGACGGAAGGCACTTAT
1 TTTACTTGCTT-TTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* * *
5598 TTTACTTGTCGTTTCCCAAAACACCCTTCCCGGACGGAAGGCACTTTT
1 TTTACTTG-CTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* *
5646 TTTACCTGCTATTTCCAAAAAACGCCCTTCCCGGACGGAAGGCACCTT-T
1 TTTACTTGCT-TTTCC-CAAAACGCCCTTCCCGGACGGAAGGCA-CTTAT
* * *
5695 TTTACCTGCTTTTTCCAAAAAACGCCCTTCCCGGACAGAAGGC
1 TTTACTTGC-TTTTCC-CAAAACGCCCTTCCCGGACGGAAGGC
5738 GTTCATGTTT
Statistics
Matches: 253, Mismatches: 24, Indels: 13
0.87 0.08 0.04
Matches are distributed among these distances:
47 2 0.01
48 178 0.70
49 69 0.27
50 4 0.02
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (47 bp):
TTTACTTGCTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
Found at i:12973 original size:19 final size:18
Alignment explanation
Indices: 12940--12975 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12930 TTGAAATAAT
12940 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
12958 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
12976 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.