Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006810.1 Corchorus capsularis cultivar CVL-1 contig06831, 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: 25434
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:5380 original size:22 final size:24
Alignment explanation
Indices: 5346--5407 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 24
5336 ATTCACTGCT
* *
5346 TTTTAATTAATTGTTTTCTT-TAA
1 TTTTACTTGATTGTTTTCTTATAA
*
5369 TTTT-CTTGATTGCTTTCTTAGTAA
1 TTTTACTTGATTGTTTTCTTA-TAA
*
5393 TTTTACTTGTTTGTT
1 TTTTACTTGATTGTT
5408 AGATTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 12 0.39
23 4 0.13
24 7 0.23
25 8 0.26
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.65
Consensus pattern (24 bp):
TTTTACTTGATTGTTTTCTTATAA
Found at i:6319 original size:21 final size:21
Alignment explanation
Indices: 6293--6341 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6283 GCGCTGGGCG
* *
6293 CCCATGTGGTATGCTTGGCAC
1 CCCATGTGGTATGCCTCGCAC
* *
6314 CCCATGTGGTTTGCCTCGCGC
1 CCCATGTGGTATGCCTCGCAC
6335 CCCATGT
1 CCCATGT
6342 ACTCCAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCAC
Found at i:14839 original size:21 final size:21
Alignment explanation
Indices: 14815--14863 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
14805 GCGTTGGGCG
* *
14815 CCCATGTGGTATGCTTGGCAC
1 CCCATGTGGTATGCCTCGCAC
* *
14836 CCCATGTGGTTTGCCTCGCGC
1 CCCATGTGGTATGCCTCGCAC
14857 CCCATGT
1 CCCATGT
14864 ACTCCAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCAC
Found at i:16048 original size:32 final size:32
Alignment explanation
Indices: 15998--16065 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
15988 AATAAAGTAA
*
15998 ACTATTTAGTGGCGTTTTTTATTAGAAACGCC
1 ACTATTTAGTGGCGTTTTTTATTAGAAAAGCC
* * *
16030 ACTA-TTAGTGGTGTTTTTTTCTTTGAAAAGCC
1 ACTATTTAGTGGCG-TTTTTTATTAGAAAAGCC
16062 ACTA
1 ACTA
16066 ATTTGACATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (32 bp):
ACTATTTAGTGGCGTTTTTTATTAGAAAAGCC
Found at i:19433 original size:31 final size:31
Alignment explanation
Indices: 19396--19457 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
19386 AGGGGCGTTT
*
19396 TTTTCCACTGAAACGCCACAATTAAGTGGTG
1 TTTTCCACGGAAACGCCACAATTAAGTGGTG
* * *
19427 TTTTCCACGGAAATGCCACTATTTAGTGGTG
1 TTTTCCACGGAAACGCCACAATTAAGTGGTG
19458 CTTCTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (31 bp):
TTTTCCACGGAAACGCCACAATTAAGTGGTG
Found at i:19636 original size:33 final size:33
Alignment explanation
Indices: 19599--19663 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
19589 GTTTAAAAAC
*
19599 GCCACTAAATAGGGGCGTTTCGTGTCTAGAAAT
1 GCCACTAAATAGGGGCATTTCGTGTCTAGAAAT
*
19632 GCCACTAAATAGGGGCATTTTGTGTCTAGAAA
1 GCCACTAAATAGGGGCATTTCGTGTCTAGAAA
19664 CGCCCTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (33 bp):
GCCACTAAATAGGGGCATTTCGTGTCTAGAAAT
Found at i:21418 original size:21 final size:21
Alignment explanation
Indices: 21394--21465 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
21384 TTACTATTTC
21394 ACTGATTATTCTTTACTTTGT
1 ACTGATTATTCTTTACTTTGT
21415 ACTGATTACTAT-TTTACTCTTGT
1 ACTGATTA-T-TCTTTACT-TTGT
*
21438 --TGATTA-TCTTCTTACTTTTT
1 ACTGATTATTC-T-TTACTTTGT
21458 ACTGATTA
1 ACTGATTA
21466 CCATTTTACT
Statistics
Matches: 42, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
18 1 0.02
20 4 0.10
21 19 0.45
22 13 0.31
23 5 0.12
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (21 bp):
ACTGATTATTCTTTACTTTGT
Found at i:21430 original size:22 final size:21
Alignment explanation
Indices: 21384--21763 Score: 218
Period size: 22 Copynumber: 17.1 Consensus size: 21
21374 TTGATTACCA
*
21384 TTACTATTTCACTGATTA-TTCT
1 TTACT-TTTTACTGATTACTT-T
*
21406 TTACTTTGTACTGATTACTATT
1 TTACTTTTTACTGATTACT-TT
* *
21428 TTACTCTTGT--TGATTATCTTC
1 TTACT-TTTTACTGATTA-CTTT
*
21449 TTACTTTTTACTGATTACCATT
1 TTACTTTTTACTGATTA-CTTT
21471 TTACTCTTTTACTGATTACTATTTT
1 TTACT-TTTTACTGATTAC---TTT
*
21496 CTGCTCCATTTTTACTGATTACTCTT
1 -T--TAC-TTTTTACTGATTACT-TT
*
21522 TTAGTTTTTACTGATTACCTTT
1 TTACTTTTTACTGATTA-CTTT
*
21544 TT-GTGTTTTACTGATTATCTTT
1 TTACT-TTTTACTGATTA-CTTT
* * *
21566 TTACTTCTTGCAGATTAGCTTT
1 TTACTTTTTACTGATTA-CTTT
** *
21588 TTACACTTTACTGATCACCTTT
1 TTACTTTTTACTGATTA-CTTT
* * *
21610 TTAC-TCTTACTGGTTTCCTTT
1 TTACTTTTTACT-GATTACTTT
* *
21631 TTACTTCTTACTTATTACTTTTT
1 TTACTTTTTACTGATTAC--TTT
* *
21654 TTAC-TCTTACTGATTACTAT
1 TTACTTTTTACTGATTACTTT
*
21674 TTACTTTTTACTGACTACTATT
1 TTACTTTTTACTGATTACT-TT
* *
21696 TTACTCTTGT--TGATTACCTTC
1 TTACT-TTTTACTGATTA-CTTT
21717 TTACTTTTTACTGATTACTATT
1 TTACTTTTTACTGATTACT-TT
*
21739 TTACTCTTTTTCTGATTACTCTT
1 TTACT-TTTTACTGATTACT-TT
21762 TT
1 TT
21764 TACCCTTTCA
Statistics
Matches: 284, Mismatches: 44, Indels: 59
0.73 0.11 0.15
Matches are distributed among these distances:
20 12 0.04
21 65 0.23
22 136 0.48
23 48 0.17
25 4 0.01
26 3 0.01
28 15 0.05
29 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (21 bp):
TTACTTTTTACTGATTACTTT
Found at i:21463 original size:43 final size:43
Alignment explanation
Indices: 21406--21746 Score: 219
Period size: 43 Copynumber: 7.7 Consensus size: 43
21396 TGATTATTCT
*
21406 TTACTTTGTACTGATTACTATTTTACTCTTGTTGATTATCTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGTTGATTATCTTC
* * *
21449 TTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGT--TGA-T--TATCTTC
* * * * *
21497 TGCTCCATTTTTACTGATTACTCTTTTAGT-TTTTACTGATTACCTT-
1 T--TAC-TTTTTACTGATTACTATTTTACTCTTGT--TGATTATCTTC
** ** * *
21543 TTTGTGTTTTACTGATTATCT-TTTTACTTCTTGCAGATTAGCTTT
1 TTACT-TTTTACTGATTA-CTATTTTAC-TCTTGTTGATTATCTTC
** * ** * *
21588 TTACACTTTACTGATCACCT-TTTTACTCTTACTGGTT-TCCTTT
1 TTACTTTTTACTGATTA-CTATTTTACTCTTGTTGATTAT-CTTC
* * * **
21631 TTACTTCTTACTTATTACTTTTTTTACTCTTACTGATTA-CTAT-
1 TTACTTTTTACTGATTAC-TATTTTACTCTTGTTGATTATCT-TC
* *
21674 TTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGTTGATTATCTTC
21717 TTACTTTTTACTGATTACTATTTTACTCTT
1 TTACTTTTTACTGATTACTATTTTACTCTT
21747 TTTCTGATTA
Statistics
Matches: 238, Mismatches: 40, Indels: 40
0.75 0.13 0.13
Matches are distributed among these distances:
42 19 0.08
43 103 0.43
44 61 0.26
45 8 0.03
46 4 0.02
47 4 0.02
48 7 0.03
49 1 0.00
50 11 0.05
51 20 0.08
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (43 bp):
TTACTTTTTACTGATTACTATTTTACTCTTGTTGATTATCTTC
Found at i:21489 original size:15 final size:15
Alignment explanation
Indices: 21471--21524 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
21461 GATTACCATT
21471 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
21486 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* *
21499 CTCCAT-TTTTACTGA
1 TTAC-TCTTTTACTGA
21514 TTACTCTTTTA
1 TTACTCTTTTA
21525 GTTTTTACTG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
13 6 0.20
14 8 0.27
15 16 0.53
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.56
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:21685 original size:65 final size:65
Alignment explanation
Indices: 21549--21766 Score: 151
Period size: 65 Copynumber: 3.3 Consensus size: 65
21539 CCTTTTTGTG
* *
21549 TTTTACTGATTATCTTTTTACTTCTTGCAGATTAGCTTTTTACACTTTACTGATCACCTTTTTAC
1 TTTTACTGATTATCTTTTTACTTCTTACAGATTAGCTTTTTACACTTTACTGATCACCTATTTAC
* * ** ** *
21614 TCTTACTGGTT-TCCTTTTTACTTCTTACTTATTA-CTTTTTTTACTCTTACTGATTA-CTATTT
1 TTTTACTGATTAT-CTTTTTACTTCTTACAGATTAGCTTTTTACACT-TTACTGATCACCTATTT
21676 AC
64 AC
* *** * * ** *
21678 TTTTTACTGACTA-CTATTTTAC-TCTTGTTGATTACCTTCTTACTTTTTACTGATTA-CTATTT
1 -TTTTACTGATTATCT-TTTTACTTCTTACAGATTAGCTTTTTACACTTTACTGATCACCTA-TT
21740 TACTC
63 TA--C
*
21745 TTTTTCTGATTACTCTTTTTAC
1 TTTTACTGATTA-TCTTTTTAC
21767 CCTTTCAGGT
Statistics
Matches: 120, Mismatches: 22, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
64 41 0.34
65 60 0.50
66 10 0.08
67 7 0.06
68 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.56
Consensus pattern (65 bp):
TTTTACTGATTATCTTTTTACTTCTTACAGATTAGCTTTTTACACTTTACTGATCACCTATTTAC
Found at i:22045 original size:55 final size:55
Alignment explanation
Indices: 21984--22219 Score: 339
Period size: 55 Copynumber: 4.3 Consensus size: 55
21974 CATTTTAACT
*
21984 CTTAATTA-TCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
* * * * * *
22039 CTTAATTACTGATTTACTGATTTCTAATACCTTGACTCTAATTAATTTCCTTTTA
1 CTTAATTACTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
* *
22094 CTTAATTACTGATTTACTGATTACTGCTACTTTGACCCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
* *
22149 CTTAATTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATTTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTACTACTTTGACTC-TGATTAATCTCTTTTTA
22205 CTTAATTTACTGATT
1 CTTAA-TTACTGATT
22220 GCCCCCTTTC
Statistics
Matches: 162, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
55 131 0.81
56 22 0.14
57 9 0.06
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:22949 original size:51 final size:51
Alignment explanation
Indices: 22868--23212 Score: 240
Period size: 51 Copynumber: 6.8 Consensus size: 51
22858 AAAGTAACAT
* * *
22868 TTTATTTACTAATTACT-TAAA-AGTTCAATCTTTCATTCAAATGTTAAAAC
1 TTTATTTACTAATTACTCTAAAGA-TTCAATCTTTTATTCAAACGTTAAATC
* * ** * * * *
22918 TTTATTTAATAATCACTCTAAAGATTCAATCTTTTACCCAAACATGACATT
1 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTATTCAAACGTTAAATC
* * * * *
22969 TTTACTTACCAATTAC-ATAAAAATTCAATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTATTCAAACGTTAAATC
* * * * *
23019 TTCATTTACTAATTACTCTAAAGATTCAATCTTTTACTCAAA-GATGACATTT
1 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTATTCAAACG-TTA-AATC
* * *
23071 TTTATTTACCAATTAC-ATAAAAATTCAATCTTTTATTCAAA-GCTTAAAAT-
1 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTATTCAAACG-TT-AAATC
* * * * * * * * * *
23121 TTTATTTGCTAATCATTTTAAAAATTCAATGTTTTACTCAAA-GATGACATT
1 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTATTCAAACG-TTAAATC
* * *
23172 TTTATTTACCAATTAC-ATAAAAATTCAATCTTTTATTCAAA
1 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTATTCAAA
23213 TGATAAACCT
Statistics
Matches: 229, Mismatches: 58, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
50 91 0.40
51 120 0.52
52 18 0.08
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.42
Consensus pattern (51 bp):
TTTATTTACTAATTACTCTAAAGATTCAATCTTTTATTCAAACGTTAAATC
Found at i:22972 original size:101 final size:101
Alignment explanation
Indices: 22867--23219 Score: 510
Period size: 101 Copynumber: 3.5 Consensus size: 101
22857 AAAAGTAACA
* * * * *
22867 TTTTATTTACTAATTACTTAAAAGTTCAATCTTTCATTCAAATGTTAAAACTTTATTTAATAATC
1 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAATGTTAAAACTTTATTTACTAATC
* *
22932 ACTCTAAAGATTCAATCTTTTACCCAAACATGACAT
66 ACTCTAAAGATTCAATCTTTTACTCAAAGATGACAT
* * * * *
22968 TTTTACTTACCAATTACATAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTCATTTACTAATT
1 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAATGTTAAAACTTTATTTACTAATC
23033 ACTCTAAAGATTCAATCTTTTACTCAAAGATGACATT
66 ACTCTAAAGATTCAATCTTTTACTCAAAGATGACA-T
* *
23070 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAA-GCTTAAAATTTTATTTGCTAAT
1 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAATG-TTAAAACTTTATTTACTAAT
* * * *
23134 CATTTTAAAAATTCAATGTTTTACTCAAAGATGACAT
65 CACTCTAAAGATTCAATCTTTTACTCAAAGATGACAT
*
23171 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAATGATAAA
1 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAATGTTAAA
23220 CCTCTTAGCC
Statistics
Matches: 226, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
101 136 0.60
102 90 0.40
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.42
Consensus pattern (101 bp):
TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAATGTTAAAACTTTATTTACTAATC
ACTCTAAAGATTCAATCTTTTACTCAAAGATGACAT
Done.