Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007653.1 Corchorus capsularis cultivar CVL-1 contig07674, 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: 15703
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Found at i:53 original size:21 final size:20
Alignment explanation
Indices: 1--71 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 20
* **
1 TATTTGACTCTTACTAATTA
1 TATTTTACTCTTACTGGTTA
* *
21 TCACTTTGCTCTTACTGGTTA
1 T-ATTTTACTCTTACTGGTTA
42 CTATTTTACTCTTACTGGTTA
1 -TATTTTACTCTTACTGGTTA
*
63 TCTTTTACT
1 TATTTTACT
72 GATTACTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 9 0.22
21 31 0.76
22 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (20 bp):
TATTTTACTCTTACTGGTTA
Found at i:77 original size:21 final size:21
Alignment explanation
Indices: 32--78 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
22 CACTTTGCTC
*
32 TTACTGGTTACTATTTTACTC
1 TTACTGGTTACTATTTTACTA
*
53 TTACTGGTTA-TCTTTTACTGA
1 TTACTGGTTACTATTTTACT-A
74 TTACT
1 TTACT
79 ATTTAGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (21 bp):
TTACTGGTTACTATTTTACTA
Found at i:119 original size:22 final size:21
Alignment explanation
Indices: 65--295 Score: 171
Period size: 22 Copynumber: 10.3 Consensus size: 21
55 ACTGGTTATC
*
65 TTTTACTGATTA-CTATTTAGT
1 TTTTACTGATTACCT-TTTACT
* *
86 CTTTGCTGATTACCTTCTTACT
1 TTTTACTGATTACCTT-TTACT
108 TTTTACTGATTACCATTTTACTT
1 TTTTACTGATTACC-TTTTAC-T
*
131 TTTTACTGATTACCATTTTCTGCTCCCTT
1 TTTTACTGATTACC---TT-T--T-AC-T
160 TTTTACTGATTACTCTTTTACT
1 TTTTACTGATTAC-CTTTTACT
** *
182 TTTTACTGATTGTCTTTTGCT
1 TTTTACTGATTACCTTTTACT
203 TTTTACTGATTACCTTTTTA-T
1 TTTTACTGATTACC-TTTTACT
*
224 TTCTTACTGATTAGCTTTTTACT
1 TT-TTACTGATTA-CCTTTTACT
* *
247 CTTTACTGATCACCTTTTCAC-
1 TTTTACTGATTACCTTTT-ACT
* *
268 TCTTACTGATTTCCTTTTACT
1 TTTTACTGATTACCTTTTACT
*
289 TCTTACT
1 TTTTACT
296 TGTTACTTTT
Statistics
Matches: 171, Mismatches: 22, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
20 2 0.01
21 59 0.35
22 64 0.37
23 21 0.12
24 1 0.01
25 2 0.01
26 2 0.01
27 2 0.01
28 1 0.01
29 16 0.09
30 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTACTGATTACCTTTTACT
Found at i:143 original size:15 final size:15
Alignment explanation
Indices: 125--181 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
115 GATTACCATT
125 TTACTTTTTTACTGA
1 TTACTTTTTTACTGA
** *
140 TTACCATTTT-CTGC
1 TTACTTTTTTACTGA
**
154 TCCCTTTTTTACTGA
1 TTACTTTTTTACTGA
*
169 TTACTCTTTTACT
1 TTACTTTTTTACT
182 TTTTACTGAT
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
14 9 0.30
15 21 0.70
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.56
Consensus pattern (15 bp):
TTACTTTTTTACTGA
Found at i:184 original size:21 final size:20
Alignment explanation
Indices: 160--295 Score: 119
Period size: 21 Copynumber: 6.3 Consensus size: 20
150 CTGCTCCCTT
160 TTTTACTGATTACTCTTTTAC
1 TTTTACTGATTAC-CTTTTAC
** *
181 TTTTTACTGATTGTCTTTTGC
1 -TTTTACTGATTACCTTTTAC
*
202 TTTTTACTGATTACCTTTTTAT
1 -TTTTACTGATTACC-TTTTAC
*
224 TTCTTACTGATTAGCTTTTTAC
1 TT-TTACTGATTA-CCTTTTAC
*
246 TCTTTACTGATCACCTTTTCAC
1 T-TTTACTGATTACCTTTT-AC
* *
268 TCTTACTGATTTCCTTTTAC
1 TTTTACTGATTACCTTTTAC
288 TTCTTACT
1 TT-TTACT
296 TGTTACTTTT
Statistics
Matches: 93, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
20 3 0.03
21 45 0.48
22 43 0.46
23 2 0.02
ACGTcount: A:0.16, C:0.21, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACTGATTACCTTTTAC
Found at i:222 original size:43 final size:41
Alignment explanation
Indices: 159--314 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 41
149 TCTGCTCCCT
*
159 TTTTTACTGATTACTCTTTTACTTTTTACTGATTGTCTTTTGC
1 TTTTTACTGATTACT-TTTTA-TTTTTACTGATTGTCTTTTAC
202 TTTTTACTGATTACCTTTTTATTTCTTACTGATTAG-CTTTTTAC
1 TTTTTACTGATTA-CTTTTTATTT-TTACTGATT-GTC-TTTTAC
* * * * *
246 TCTTTACTGATCACCTTTTCACTCTTACTGATT-TCCTTTTAC
1 TTTTTACTGATTA-CTTTTTATTTTTACTGATTGT-CTTTTAC
*
288 TTCTTACTTG-TTACTTTTT-TTTTTACT
1 TTTTTAC-TGATTACTTTTTATTTTTACT
315 CTTACTGATT
Statistics
Matches: 94, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
40 6 0.06
41 5 0.05
42 16 0.17
43 40 0.43
44 27 0.29
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.59
Consensus pattern (41 bp):
TTTTTACTGATTACTTTTTATTTTTACTGATTGTCTTTTAC
Found at i:332 original size:25 final size:26
Alignment explanation
Indices: 282--332 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
272 ACTGATTTCC
* *
282 TTTTACTTCTTACTTGTTACTTTTTT
1 TTTTACTTCTTACTTGTTAATATTTT
308 TTTTAC-TCTTAC-TGATTAATATTTT
1 TTTTACTTCTTACTTG-TTAATATTTT
333 ACTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 14 0.64
26 6 0.27
ACGTcount: A:0.18, C:0.14, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTACTTCTTACTTGTTAATATTTT
Found at i:706 original size:32 final size:32
Alignment explanation
Indices: 644--738 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 32
634 AACCCTTAAT
* * *
644 TATCGATTCACTGATTACCATTTTTACCTTGGC
1 TATCAATTTACTGATTA-CATTTTTACCTTGCC
*
677 TCTCTAA-TTACTGATTA-ATTTCTTACCTTGCC
1 TATC-AATTTACTGATTACATTT-TTACCTTGCC
709 TATCAATTTACTGATTACTATCTTTTACCT
1 TATCAATTTACTGATTAC-AT-TTTTACCT
739 GATTACTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
31 6 0.12
32 22 0.43
33 12 0.24
34 9 0.18
35 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.46
Consensus pattern (32 bp):
TATCAATTTACTGATTACATTTTTACCTTGCC
Found at i:812 original size:15 final size:16
Alignment explanation
Indices: 786--815 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
776 ATTAATCTCT
786 TTTACTTAATTACTGA
1 TTTACTTAATTACTGA
802 TTTAC-TAATTACTG
1 TTTACTTAATTACTG
816 TTACTTTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (16 bp):
TTTACTTAATTACTGA
Found at i:856 original size:26 final size:26
Alignment explanation
Indices: 827--916 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
817 TACTTTGACT
*
827 CTGATTTACCTCTTTTTACTTAATTA
1 CTGATTTACATCTTTTTACTTAATTA
* * *
853 CTGATTTACTAATCACTATTACCTTAACT-
1 CTGATTTAC--ATC-TTTTTA-CTTAATTA
* **
882 CTGATTAATTTCTTTTTACTTAATTA
1 CTGATTTACATCTTTTTACTTAATTA
908 CTGATTTAC
1 CTGATTTAC
917 TGACTTCTAT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 6 0.13
26 20 0.43
27 2 0.04
28 2 0.04
29 11 0.23
30 6 0.13
ACGTcount: A:0.27, C:0.19, G:0.04, T:0.50
Consensus pattern (26 bp):
CTGATTTACATCTTTTTACTTAATTA
Found at i:861 original size:55 final size:55
Alignment explanation
Indices: 731--917 Score: 277
Period size: 55 Copynumber: 3.4 Consensus size: 55
721 GATTACTATC
* * *
731 TTTTACCTGATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTC-
1 TTTTACTTAATTACTGATTTACTAATTACTATTACCTTAACTCTGATTAATCTCT
* * * * *
785 TTTTACTTAATTACTGATTTACTAATTACTGTTACTTTGACTCTGATTTACCTCT
1 TTTTACTTAATTACTGATTTACTAATTACTATTACCTTAACTCTGATTAATCTCT
* *
840 TTTTACTTAATTACTGATTTACTAATCACTATTACCTTAACTCTGATTAATTTCT
1 TTTTACTTAATTACTGATTTACTAATTACTATTACCTTAACTCTGATTAATCTCT
895 TTTTACTTAATTACTGATTTACT
1 TTTTACTTAATTACTGATTTACT
918 GACTTCTATC
Statistics
Matches: 117, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 46 0.39
55 71 0.61
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (55 bp):
TTTTACTTAATTACTGATTTACTAATTACTATTACCTTAACTCTGATTAATCTCT
Found at i:940 original size:109 final size:107
Alignment explanation
Indices: 715--941 Score: 289
Period size: 109 Copynumber: 2.1 Consensus size: 107
705 TGCCTATCAA
* * *
715 TTTACTGA-TTACTATCTTTTACCTGATTACTGATTTACTGATTACTATTACCTTAACTCTGATT
1 TTTACTGATTTACTATCTTTTACCTAATTACTGATTTACTAATCACTATTACCTTAACTCTGATT
* *
779 AATCTCTTTTACTTAATTACTGATTTACTAATTACTGTTACT
66 AATCTCTTTTACTTAATTACTGATTTACTAATTACTATCACT
* * *
821 TTGACTCTGATTTAC-CTCTTTTTACTTAATTACTGATTTACTAATCACTATTACCTTAACTCTG
1 TTTA--CTGATTTACTATC-TTTTACCTAATTACTGATTTACTAATCACTATTACCTTAACTCTG
* *
885 ATTAATTTCTTTTTACTTAATTACTGATTTACTGACTT-CTATCACT
63 ATTAATCTC-TTTTACTTAATTACTGATTTACT-AATTACTATCACT
931 CTTTACTGATT
1 -TTTACTGATT
942 ACCATTTTAC
Statistics
Matches: 103, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
106 3 0.03
108 6 0.06
109 59 0.57
110 29 0.28
111 6 0.06
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (107 bp):
TTTACTGATTTACTATCTTTTACCTAATTACTGATTTACTAATCACTATTACCTTAACTCTGATT
AATCTCTTTTACTTAATTACTGATTTACTAATTACTATCACT
Done.