Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012058.1 Corchorus capsularis cultivar CVL-1 contig12079, 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: 13619
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Found at i:2498 original size:62 final size:62
Alignment explanation
Indices: 2384--2643 Score: 409
Period size: 62 Copynumber: 4.2 Consensus size: 62
2374 AACTTCATAA
2384 GAACTGTCTTCA-AATCCT-TCTTCGTGAACTGTCTT-AGATTCACTCTAAAATATCTTTTAG
1 GAACTGTCTTCAGAA-CCTATCTTCGTGAACTGTCTTCAGATTCACTCTAAAATATCTTTTAG
*
2444 GAACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTCAGATTCACTCTCAAATATCTTTTAG
1 GAACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTCAGATTCACTCTAAAATATCTTTTAG
* * * *
2506 GAACTATCTTCCGAACCTATCTTCGTGAATTGTCTTCAGATTCACTCTAAAATATCATTTAG
1 GAACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTCAGATTCACTCTAAAATATCTTTTAG
* * * *
2568 GAACTGTCTTCAGAACCTATCCTCGTGAACTGTCTTCAGATTCACTGTCAAATATCTTTCAG
1 GAACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTCAGATTCACTCTAAAATATCTTTTAG
2630 GAACTGTCTTCAGA
1 GAACTGTCTTCAGA
2644 TCCATGGACT
Statistics
Matches: 183, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
60 15 0.08
61 19 0.10
62 149 0.81
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (62 bp):
GAACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTCAGATTCACTCTAAAATATCTTTTAG
Found at i:12794 original size:15 final size:14
Alignment explanation
Indices: 12754--12927 Score: 58
Period size: 15 Copynumber: 11.6 Consensus size: 14
12744 GCTGACTCCT
12754 TTTACTTTTAC-TC
1 TTTACTTTTACTTC
*
12767 TTTAACTGATTACTTC
1 TTT-ACT-TTTACTTC
12783 TCTTACTTTTAC-TC
1 T-TTACTTTTACTTC
*
12797 -TTA--ATTACTTC
1 TTTACTTTTACTTC
* *
12808 TTTTACTTTTGCTTTT
1 -TTTACTTTTAC-TTC
*
12824 TTGTACTGATTACTTC
1 TT-TACT-TTTACTTC
12840 TTTTACTTTTACTCTTTCAC
1 -TTTACTTTTA--C-TT--C
*
12860 TTCTACTGATTACTTC
1 TT-TACT-TTTACTTC
12876 TTTTACTTTTAC-TC
1 -TTTACTTTTACTTC
12890 TTTTACTTTTACTT-
1 -TTTACTTTTACTTC
*
12904 TTTACTGATTACCTT-
1 TTTACT-TTTA-CTTC
12919 TTTACTTTT
1 TTTACTTTT
12928 TAATGATTAC
Statistics
Matches: 123, Mismatches: 14, Indels: 47
0.67 0.08 0.26
Matches are distributed among these distances:
10 4 0.03
11 2 0.02
12 3 0.02
13 12 0.10
14 24 0.20
15 30 0.24
16 23 0.19
17 10 0.08
18 4 0.03
19 3 0.02
20 5 0.04
21 3 0.02
ACGTcount: A:0.17, C:0.20, G:0.03, T:0.60
Consensus pattern (14 bp):
TTTACTTTTACTTC
Found at i:12874 original size:36 final size:35
Alignment explanation
Indices: 12800--12902 Score: 140
Period size: 36 Copynumber: 3.0 Consensus size: 35
12790 TTTACTCTTA
* *
12800 ATTACTTCTTTTACTTTTGCT-TTT--TTGTACTG
1 ATTACTTCTTTTACTTTTACTCTTTACTTCTACTG
12832 ATTACTTCTTTTACTTTTACTCTTTCACTTCTACTG
1 ATTACTTCTTTTACTTTTACTCTTT-ACTTCTACTG
*
12868 ATTACTTCTTTTACTTTTACTCTTTTACTTTTACT
1 ATTACTTCTTTTACTTTTACTC-TTTACTTCTACT
12903 TTTTACTGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
32 20 0.32
33 3 0.05
36 37 0.59
37 3 0.05
ACGTcount: A:0.16, C:0.20, G:0.04, T:0.60
Consensus pattern (35 bp):
ATTACTTCTTTTACTTTTACTCTTTACTTCTACTG
Found at i:12908 original size:7 final size:7
Alignment explanation
Indices: 12876--12929 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
12866 TGATTACTTC
12876 TTTTAC-
1 TTTTACT
12882 TTTTACT
1 TTTTACT
12889 CTTTTAC-
1 -TTTTACT
12896 TTTTACT
1 TTTTACT
12903 TTTTACT
1 TTTTACT
**
12910 GATTACCT
1 TTTTA-CT
12918 TTTTACT
1 TTTTACT
12925 TTTTA
1 TTTTA
12930 ATGATTACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 12 0.30
7 17 0.43
8 11 0.28
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTTACT
Found at i:12909 original size:36 final size:36
Alignment explanation
Indices: 12752--12909 Score: 130
Period size: 36 Copynumber: 4.4 Consensus size: 36
12742 TTGCTGACTC
* * *
12752 CTTTTAC-TTTTAC-TCTTTAACTGATTACTTCTCTTA
1 CTTTTACTTTTTACTTCTTTTACT-TTTAC-TCTTTTA
*
12788 CTTTTACTCTTAATTACTTCTTTTACTTTT--GCTTTT-
1 CTTTTACT-TT--TTACTTCTTTTACTTTTACTCTTTTA
* ** *
12824 -TTGTACTGATTACTTCTTTTACTTTTACTCTTTCA
1 CTTTTACTTTTTACTTCTTTTACTTTTACTCTTTTA
* **
12859 CTTCTACTGATTACTTCTTTTACTTTTACTCTTTTA
1 CTTTTACTTTTTACTTCTTTTACTTTTACTCTTTTA
12895 CTTTTACTTTTTACT
1 CTTTTACTTTTTACT
12910 GATTACCTTT
Statistics
Matches: 99, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
32 17 0.17
34 4 0.04
35 6 0.06
36 52 0.53
37 4 0.04
38 2 0.02
40 6 0.06
41 8 0.08
ACGTcount: A:0.16, C:0.21, G:0.03, T:0.59
Consensus pattern (36 bp):
CTTTTACTTTTTACTTCTTTTACTTTTACTCTTTTA
Found at i:12915 original size:14 final size:14
Alignment explanation
Indices: 12752--12920 Score: 62
Period size: 14 Copynumber: 11.4 Consensus size: 14
12742 TTGCTGACTC
*
12752 CTTTTACTTTTACT
1 CTTTTACTATTACT
*
12766 CTTTAACTGATTACTT
1 CTTTTACT-ATTAC-T
* *
12782 CTCTTACTTTTACT
1 CTTTTACTATTACT
12796 C--TTA--ATTACTT
1 CTTTTACTATTAC-T
* *
12807 CTTTTACTTTTGCTT
1 CTTTTACTATTAC-T
*
12822 TTTTGTACTGATTACTT
1 CTTT-TACT-ATTAC-T
*
12839 CTTTTACTTTTACT
1 CTTTTACTATTACT
12853 CTTTCACTTCTACTGATTACTT
1 C--T---TT-TACT-ATTAC-T
*
12875 CTTTTACTTTTACT
1 CTTTTACTATTACT
*
12889 CTTTTACTTTTACT
1 CTTTTACTATTACT
12903 -TTTTACTGATTAC-
1 CTTTTACT-ATTACT
12916 CTTTT
1 CTTTT
12921 TACTTTTTAA
Statistics
Matches: 120, Mismatches: 16, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
10 4 0.03
11 2 0.02
12 3 0.03
13 10 0.08
14 34 0.28
15 24 0.20
16 20 0.17
17 10 0.08
19 2 0.02
20 5 0.04
21 4 0.03
22 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.04, T:0.59
Consensus pattern (14 bp):
CTTTTACTATTACT
Found at i:12919 original size:21 final size:21
Alignment explanation
Indices: 12848--13096 Score: 174
Period size: 21 Copynumber: 11.8 Consensus size: 21
12838 TCTTTTACTT
*
12848 TTACTCTTTCACTTC-TACTGA
1 TTAC-CTTTTACTTCTTACTGA
**
12869 TTACTTCTTTTACTT-TTACTCTT
1 TTAC--CTTTTACTTCTTACT-GA
*
12892 TTA-CTTTTACTTTTTACTGA
1 TTACCTTTTACTTCTTACTGA
* *
12912 TTACCTTTTTACTTTTTAATGA
1 TTACC-TTTTACTTCTTACTGA
* *
12934 TTACC-ATTGCTTCTTACTGA
1 TTACCTTTTACTTCTTACTGA
* *
12954 TTA-CTATTACTTTTTTACTGA
1 TTACCTTTTAC-TTCTTACTGA
*
12975 TTACTGTTTTAC-TCTTACTGA
1 TTAC-CTTTTACTTCTTACTGA
* *
12996 TTACCTTTTTCTTCTTCACTAA
1 TTACCTTTTACTTCTT-ACTGA
*
13018 TTACTCTCTTAC-TCTTACTGA
1 TTAC-CTTTTACTTCTTACTGA
* * *
13039 CTACTTTTTACTT-TGTACTTA
1 TTACCTTTTACTTCT-TACTGA
*
13060 TTACTATTTTAC-TCTTACTGA
1 TTAC-CTTTTACTTCTTACTGA
13081 TTACCTTTTACTTCTT
1 TTACCTTTTACTTCTT
13097 TTCCTTAATT
Statistics
Matches: 181, Mismatches: 29, Indels: 36
0.74 0.12 0.15
Matches are distributed among these distances:
19 1 0.01
20 47 0.26
21 68 0.38
22 52 0.29
23 13 0.07
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.55
Consensus pattern (21 bp):
TTACCTTTTACTTCTTACTGA
Found at i:12979 original size:15 final size:14
Alignment explanation
Indices: 12954--12994 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
12944 TTCTTACTGA
*
12954 TTACTATTACTTTT
1 TTACTATTACTGTT
12968 TTACTGATTACTGTT
1 TTACT-ATTACTGTT
*
12983 TTACTCTTACTG
1 TTACTATTACTG
12995 ATTACCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (14 bp):
TTACTATTACTGTT
Found at i:12985 original size:85 final size:86
Alignment explanation
Indices: 12896--13096 Score: 234
Period size: 85 Copynumber: 2.4 Consensus size: 86
12886 ACTCTTTTAC
* * * * *
12896 TTTTACTTTTTACTGATTACCTTTTTACTT-TTTAATGATTAC-C-ATTGCTTCTTACTGATTAC
1 TTTTAC-TCTTACTGATTACCTTTTTACTTCTTCAATAATTACTCTATTAC-TCTTACTGACTAC
* *
12958 -TATTACTTTTTTACTGATTACTG
64 TTATTAC-TTTGTACTGATTACTA
* *
12981 TTTTACTCTTACTGATTACCTTTTT-CTTCTTCACTAATTACTCTCTTACTCTTACTGACTACTT
1 TTTTACTCTTACTGATTACCTTTTTACTTCTTCAATAATTACTCTATTACTCTTACTGACTACTT
* *
13045 TTTACTTTGTACTTATTACTA
66 ATTACTTTGTACTGATTACTA
13066 TTTTACTCTTACTGATTACC-TTTTACTTCTT
1 TTTTACTCTTACTGATTACCTTTTTACTTCTT
13097 TTCCTTAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
83 3 0.03
84 31 0.31
85 58 0.58
86 8 0.08
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (86 bp):
TTTTACTCTTACTGATTACCTTTTTACTTCTTCAATAATTACTCTATTACTCTTACTGACTACTT
ATTACTTTGTACTGATTACTA
Found at i:13252 original size:38 final size:38
Alignment explanation
Indices: 13195--13364 Score: 227
Period size: 38 Copynumber: 4.5 Consensus size: 38
13185 ATTACTATTT
* *
13195 TTACCTTGACTCTTAATTATCAATTTTACTGATCACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
* * *
13233 TTACTTTGACTCTTGATTATAAATTTTACTGGTTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
13271 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
* * *
13309 TTACTTTGACTCTTAATTACTTAA-TTCACTGGTTACTA
1 TTACTTTGACTCTTAATTA-TCAATTTTACTGATTACTA
*
13347 TTA-TCTTGACTTTTAATT
1 TTACT-TTGACTCTTAATT
13365 TATTGGGGTA
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
37 1 0.01
38 114 0.97
39 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.49
Consensus pattern (38 bp):
TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
Found at i:13284 original size:76 final size:76
Alignment explanation
Indices: 13195--13364 Score: 254
Period size: 76 Copynumber: 2.2 Consensus size: 76
13185 ATTACTATTT
* *
13195 TTACCTTGACTCTTAATTATCAATTTTACTGATCACTATTACTTTGACTCTTGATTA-TAAATTT
1 TTACTTTGACTCTTAATTATCAATTTTACTGATCACTATTACTTTGACTCTTAATTACTAAA-TT
*
13259 TACTGGTTACTA
65 CACTGGTTACTA
* *
13271 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGACTCTTAATTACTTAATTC
1 TTACTTTGACTCTTAATTATCAATTTTACTGATCACTATTACTTTGACTCTTAATTACTAAATTC
13336 ACTGGTTACTA
66 ACTGGTTACTA
*
13347 TTA-TCTTGACTTTTAATT
1 TTACT-TTGACTCTTAATT
13365 TATTGGGGTA
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
75 1 0.01
76 82 0.95
77 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.49
Consensus pattern (76 bp):
TTACTTTGACTCTTAATTATCAATTTTACTGATCACTATTACTTTGACTCTTAATTACTAAATTC
ACTGGTTACTA
Found at i:13329 original size:16 final size:16
Alignment explanation
Indices: 13270--13330 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 16
13260 ACTGGTTACT
13270 ATTACTTTGACTCTTA
1 ATTACTTTGACTCTTA
* *
13286 ATTATCAATTTTACTGATTA
1 ATTA-C--TTTGACT-CTTA
13306 CTATTACTTTGACTCTTA
1 --ATTACTTTGACTCTTA
13324 ATTACTT
1 ATTACTT
13331 AATTCACTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 11 0.31
17 1 0.03
18 3 0.09
19 12 0.34
20 3 0.09
21 1 0.03
22 4 0.11
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (16 bp):
ATTACTTTGACTCTTA
Done.