Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011911.1 Corchorus capsularis cultivar CVL-1 contig11932, 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: 36406
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:179 original size:20 final size:21
Alignment explanation
Indices: 154--192 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
144 AACTATTTTA
*
154 AGTA-TTTATTTTTTACTAGG
1 AGTATTTTATATTTTACTAGG
174 AGTATTTTATATTTTACTA
1 AGTATTTTATATTTTACTA
193 AGGGGGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (21 bp):
AGTATTTTATATTTTACTAGG
Found at i:409 original size:13 final size:12
Alignment explanation
Indices: 378--408 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
368 GGGTTGATGT
*
378 AAAAAAATTTTG
1 AAAAAAATTTTA
390 AAAAAAATTTTA
1 AAAAAAATTTTA
402 AAAAAAA
1 AAAAAAA
409 ACAAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
AAAAAAATTTTA
Found at i:465 original size:32 final size:33
Alignment explanation
Indices: 418--498 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 33
408 AACAAAGAAA
*
418 ATGGCTGAGCCGCCCAAACTGGGCGGCCTTG-CT
1 ATGGCT-AGCCGCCCAAACTGGGCGGCCTTGACC
* *
451 ATGGCTAGTCGCCCAAGCTGGGCGGCCTTGACC
1 ATGGCTAGCCGCCCAAACTGGGCGGCCTTGACC
*
484 ATGGCGAGCCGCCCA
1 ATGGCTAGCCGCCCA
499 GCCATTTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 22 0.52
33 20 0.48
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.16
Consensus pattern (33 bp):
ATGGCTAGCCGCCCAAACTGGGCGGCCTTGACC
Found at i:570 original size:10 final size:10
Alignment explanation
Indices: 543--573 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
533 TTTTTTAATA
543 TTAATTAGTT
1 TTAATTAGTT
553 TATAATTAGTT
1 T-TAATTAGTT
564 TTAATTAGTT
1 TTAATTAGTT
574 AATTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (10 bp):
TTAATTAGTT
Found at i:613 original size:15 final size:14
Alignment explanation
Indices: 562--654 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
552 TTATAATTAG
*
562 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
576 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
589 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
602 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
615 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
628 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
641 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
654 T
1 T
655 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:622 original size:26 final size:26
Alignment explanation
Indices: 593--660 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
583 TACTTAGTTT
593 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
619 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
645 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
661 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:649 original size:52 final size:51
Alignment explanation
Indices: 555--660 Score: 126
Period size: 52 Copynumber: 2.1 Consensus size: 51
545 AATTAGTTTA
* * *
555 TAATTAGTTTTAATTAGTTAATTAAAATTACTTAGTTTATTAGTTTATGTT
1 TAATTAGTTCTAATTAGTTAATTAAAATTACGTAGTTTATTAGTTTATGAT
* *
606 TAATTAGTATCTAATTAGTTTATTATTAATTA-GTA-TTTAATTAGTTTATGAT
1 TAATTAGT-TCTAATTAGTTAATTA-AAATTACGTAGTTT-ATTAGTTTATGAT
658 TAA
1 TAA
661 AATGAAGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 11 0.23
52 31 0.66
53 5 0.11
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (51 bp):
TAATTAGTTCTAATTAGTTAATTAAAATTACGTAGTTTATTAGTTTATGAT
Found at i:660 original size:15 final size:13
Alignment explanation
Indices: 543--654 Score: 57
Period size: 11 Copynumber: 9.0 Consensus size: 13
533 TTTTTTAATA
543 TTAATTAGTTTA-
1 TTAATTAGTTTAT
555 -TAATTAG--T-T
1 TTAATTAGTTTAT
*
564 TTAATTAGTTAAT
1 TTAATTAGTTTAT
* *
577 TAAAATTA-CTTAGT
1 T-TAATTAGTTTA-T
591 TT-ATTAGTTTATGT
1 TTAATTAGTTTA--T
605 TTAATTAG--TAT
1 TTAATTAGTTTAT
*
616 CTAATTAGTTTATT
1 TTAATTAGTTTA-T
630 ATTAATTAG--TAT
1 -TTAATTAGTTTAT
642 TTAATTAGTTTAT
1 TTAATTAGTTTAT
655 GATTAAAATG
Statistics
Matches: 76, Mismatches: 8, Indels: 31
0.66 0.07 0.27
Matches are distributed among these distances:
9 1 0.01
10 7 0.09
11 23 0.30
12 5 0.07
13 16 0.21
14 12 0.16
15 12 0.16
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (13 bp):
TTAATTAGTTTAT
Found at i:708 original size:24 final size:25
Alignment explanation
Indices: 669--728 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
659 AAAATGAAGG
*
669 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
692 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
717 GAAATTAAGTTT
1 AAAATGAAGTTT
729 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:839 original size:42 final size:42
Alignment explanation
Indices: 785--871 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
775 ATATGAACAA
785 AGGGCAAAAGTGTAAAAAGGGGAGCGGTATTTAACAAAAAGG
1 AGGGCAAAAGTGTAAAAAGGGGAGCGGTATTTAACAAAAAGG
* *
827 AGGGTAAAAGTGTAAAAAGGGGAGCGGTATTTAACAAAAGGG
1 AGGGCAAAAGTGTAAAAAGGGGAGCGGTATTTAACAAAAAGG
869 AGG
1 AGG
872 TAGTAAATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.44, C:0.06, G:0.36, T:0.15
Consensus pattern (42 bp):
AGGGCAAAAGTGTAAAAAGGGGAGCGGTATTTAACAAAAAGG
Found at i:6668 original size:2 final size:2
Alignment explanation
Indices: 6661--6690 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6651 TTGTTATTAA
6661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6691 CTCTCTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15214 original size:2 final size:2
Alignment explanation
Indices: 15207--15231 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15197 TTGTCCAAAC
15207 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15232 GAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19051 original size:2 final size:2
Alignment explanation
Indices: 19046--19078 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
19036 ACACACACAC
19046 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19079 GTATTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24551 original size:13 final size:15
Alignment explanation
Indices: 24520--24556 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
24510 TAATAAAATA
*
24520 TTTTTGAAATATA-T
1 TTTTTAAAATATATT
24534 TTTTTAAAATA-ATT
1 TTTTTAAAATATATT
24548 TTTTTAAAA
1 TTTTTAAAA
24557 AATAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTTAAAATATATT
Found at i:24630 original size:25 final size:23
Alignment explanation
Indices: 24545--24630 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 23
24535 TTTTAAAATA
24545 ATTT-TTTTAAAAAATAAATATCT
1 ATTTATTTT-AAAAATAAATATCT
** *
24568 ATTACTTATTTTTTAAATAATATATAT
1 A-T--TTATTTTAAAAATAA-ATATCT
24595 AATTTATTTTAAAAATAAATATCT
1 -ATTTATTTTAAAAATAAATATCT
24619 ATTGTATATTTA
1 ATT-TAT-TTTA
24631 TTTTCTATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
23 4 0.08
24 9 0.18
25 17 0.35
26 8 0.16
27 10 0.20
28 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (23 bp):
ATTTATTTTAAAAATAAATATCT
Found at i:25224 original size:9 final size:9
Alignment explanation
Indices: 25196--25235 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
25186 ACCCATGTAC
25196 AATACAATAA
1 AATAC-ATAA
25206 AATA-ATAA
1 AATACATAA
25214 AATACATAA
1 AATACATAA
*
25223 AATACATAC
1 AATACATAA
25232 AATA
1 AATA
25236 AAACTAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 8 0.29
9 16 0.57
10 4 0.14
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (9 bp):
AATACATAA
Found at i:25235 original size:18 final size:18
Alignment explanation
Indices: 25193--25235 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
25183 ACAACCCATG
25193 TACAATACAATAAAATAA
1 TACAATACAATAAAATAA
*
25211 TAAAATAC-ATAAAATACA
1 TACAATACAATAAAATA-A
25229 TACAATA
1 TACAATA
25236 AAACTAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (18 bp):
TACAATACAATAAAATAA
Found at i:28216 original size:80 final size:80
Alignment explanation
Indices: 28083--28242 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 80
28073 TCATGTTTCT
*
28083 CAATGAATTTCATCTTATGAAATAGTAGATGTGCATGCAATAAGAAATTTCGTCGGCATGCTATA
1 CAATGAATTTCATCTTATGAAATAGTAGAGGTGCATGCAATAAGAAATTTCGTCGGCATGCTATA
28148 GATATGATACAGACA
66 GATATGATACAGACA
* *
28163 CAATGGATTTCATCTTATGGAATAGTAGAGGTGCATGCAATAAGAAATTTCGTCGGCATGCTATA
1 CAATGAATTTCATCTTATGAAATAGTAGAGGTGCATGCAATAAGAAATTTCGTCGGCATGCTATA
28228 GATATGATACAGACA
66 GATATGATACAGACA
28243 TATAAACCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (80 bp):
CAATGAATTTCATCTTATGAAATAGTAGAGGTGCATGCAATAAGAAATTTCGTCGGCATGCTATA
GATATGATACAGACA
Found at i:34277 original size:25 final size:25
Alignment explanation
Indices: 34249--34309 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
34239 ACTAATTACC
34249 CTCTTCTGAATTAT-TACCATTTTTA
1 CTCTTCTGAATTATATACCA-TTTTA
** *
34274 CTCTTCT-TTTTCTATACCATTTTA
1 CTCTTCTGAATTATATACCATTTTA
34298 CTCTT-TGAATTA
1 CTCTTCTGAATTA
34310 CTGATCACCT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
23 1 0.04
24 15 0.54
25 12 0.43
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.54
Consensus pattern (25 bp):
CTCTTCTGAATTATATACCATTTTA
Found at i:34773 original size:34 final size:34
Alignment explanation
Indices: 34735--34846 Score: 127
Period size: 34 Copynumber: 3.2 Consensus size: 34
34725 TACCTTAACT
* **
34735 CTGATTAATTTCCTTTTACTTAATTACTGGTTTA
1 CTGATTAATCTCCTTTTACTTAATTACTAATTTA
* * *
34769 CTGATTACTGTCACTTTGACTCTGAATTA-TCAATTTA
1 CTGATTAATCTC-CTTTTACT-T-AATTACT-AATTTA
34806 CTGATTAATCTCCTTTTACTTAATTACTAATTTA
1 CTGATTAATCTCCTTTTACTTAATTACTAATTTA
34840 CTGATTA
1 CTGATTA
34847 CTATTACCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
34 28 0.43
35 9 0.14
36 9 0.14
37 19 0.29
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (34 bp):
CTGATTAATCTCCTTTTACTTAATTACTAATTTA
Found at i:34806 original size:37 final size:36
Alignment explanation
Indices: 34765--34883 Score: 136
Period size: 37 Copynumber: 3.3 Consensus size: 36
34755 TAATTACTGG
*
34765 TTTACTGATTACTGTCACTTTGACTCTGAATTATCAA
1 TTTACTGATTACTATCACTTTGACTCT-AATTATCAA
* * *
34802 TTTACTGATTAATCTC-CTTTTACT-TAATTA-CTAA
1 TTTACTGATTACTATCACTTTGACTCTAATTATC-AA
* *
34836 TTTACTGATTACTATTACCTTGACTCTTAATTATCAA
1 TTTACTGATTACTATCACTTTGACTC-TAATTATCAA
34873 TTTACTGATTA
1 TTTACTGATTA
34884 ATTTTTCTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
33 1 0.01
34 20 0.29
35 7 0.10
36 7 0.10
37 33 0.48
38 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (36 bp):
TTTACTGATTACTATCACTTTGACTCTAATTATCAA
Found at i:34820 original size:71 final size:71
Alignment explanation
Indices: 34735--34885 Score: 239
Period size: 71 Copynumber: 2.1 Consensus size: 71
34725 TACCTTAACT
* ** * *
34735 CTGATTAATTTCCTTTTACTTAATTACTGGTTTACTGATTACTGTCACTTTGACTCTGAATTATC
1 CTGATTAATCTCCTTTTACTTAATTACTAATTTACTGATTACTATCACCTTGACTCTGAATTATC
34800 AATTTA
66 AATTTA
* *
34806 CTGATTAATCTCCTTTTACTTAATTACTAATTTACTGATTACTATTACCTTGACTCTTAATTATC
1 CTGATTAATCTCCTTTTACTTAATTACTAATTTACTGATTACTATCACCTTGACTCTGAATTATC
34871 AATTTA
66 AATTTA
34877 CTGATTAAT
1 CTGATTAAT
34886 TTTTCTACCT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (71 bp):
CTGATTAATCTCCTTTTACTTAATTACTAATTTACTGATTACTATCACCTTGACTCTGAATTATC
AATTTA
Done.