Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012338.1 Corchorus capsularis cultivar CVL-1 contig12359, 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: 31725
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:973 original size:29 final size:29
Alignment explanation
Indices: 938--1009 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
928 TTATGGAGAA
938 CTCATATCTTTTATGAGTTCCTTAAAAAC
1 CTCATATCTTTTATGAGTTCCTTAAAAAC
967 CTCATATCTTTTATGAGTTCCTTAAAAAC
1 CTCATATCTTTTATGAGTTCCTTAAAAAC
996 CTCATATCTTTTAT
1 CTCATATCTTTTAT
1010 CTTTTGTAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (29 bp):
CTCATATCTTTTATGAGTTCCTTAAAAAC
Found at i:7573 original size:106 final size:106
Alignment explanation
Indices: 7449--7664 Score: 432
Period size: 106 Copynumber: 2.0 Consensus size: 106
7439 AAAAAAAGTC
7449 TTTTGGCGGCATACCAAATAATCAAATATTATTGTCACTTTGCACTCTTAAATTTATATTAACTT
1 TTTTGGCGGCATACCAAATAATCAAATATTATTGTCACTTTGCACTCTTAAATTTATATTAACTT
7514 TGCATCCAACTTTTTTATTTTGATCAAAACGCATCATAAAG
66 TGCATCCAACTTTTTTATTTTGATCAAAACGCATCATAAAG
7555 TTTTGGCGGCATACCAAATAATCAAATATTATTGTCACTTTGCACTCTTAAATTTATATTAACTT
1 TTTTGGCGGCATACCAAATAATCAAATATTATTGTCACTTTGCACTCTTAAATTTATATTAACTT
7620 TGCATCCAACTTTTTTATTTTGATCAAAACGCATCATAAAG
66 TGCATCCAACTTTTTTATTTTGATCAAAACGCATCATAAAG
7661 TTTT
1 TTTT
7665 ATTTTTATGC
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 110 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (106 bp):
TTTTGGCGGCATACCAAATAATCAAATATTATTGTCACTTTGCACTCTTAAATTTATATTAACTT
TGCATCCAACTTTTTTATTTTGATCAAAACGCATCATAAAG
Found at i:14151 original size:14 final size:14
Alignment explanation
Indices: 14128--14162 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
14118 GGTCAAGCTT
14128 TTTTTC-TTTTTTC
1 TTTTTCTTTTTTTC
14141 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
*
14155 TTATTCTT
1 TTTTTCTT
14163 CGGCTTCGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:15449 original size:31 final size:31
Alignment explanation
Indices: 15414--15473 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
15404 GTACTTGTAA
*
15414 AACTTTTGAAACGCCTATTGTACCCTTATAT
1 AACTTTTGAAACGCCTATTATACCCTTATAT
* *
15445 AACTTTTGAAACGCTTATTATATCCTTAT
1 AACTTTTGAAACGCCTATTATACCCTTAT
15474 TTGTCTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATACCCTTATAT
Found at i:15889 original size:157 final size:158
Alignment explanation
Indices: 15707--16018 Score: 547
Period size: 159 Copynumber: 2.0 Consensus size: 158
15697 TAATATAAAA
* *
15707 ATCAATTTTTAATGTATTTATTTTTTAGAGAAATCCTATTCTACTAATCTTTC-TTTTTTTTTT-
1 ATCAATTTTTAATATATTTATTTTTTAGAGAAATCCTACTCTACTAATCTTTCTTTTTTTTTTTG
* *
15770 GCCAGAGAACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTCCTTTTTCAATTTTTTG
66 GCCAGAAAACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTCCTTTTTCAATTTTTCG
15835 TTTATTTAAAAAAATTATAAACTCTACT
131 TTTATTTAAAAAAATTATAAACTCTACT
*
15863 ATCAATTTTTTAATATATTTATTTTTTAGAGAAATTCTACTCTACTAATCTTTCTTTTTTTTTTT
1 ATCAA-TTTTTAATATATTTATTTTTTAGAGAAATCCTACTCTACTAATCTTTCTTTTTTTTTTT
15928 GGCCAGAAAACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTCCTTTTTCAATTTTTC
65 GGCCAGAAAACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTCCTTTTTCAATTTTTC
*
15993 GTTTATTTAAAAGAATTATAAACTCT
130 GTTTATTTAAAAAAATTATAAACTCT
16019 TTATAATTGC
Statistics
Matches: 147, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
156 5 0.03
157 45 0.31
158 10 0.07
159 87 0.59
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (158 bp):
ATCAATTTTTAATATATTTATTTTTTAGAGAAATCCTACTCTACTAATCTTTCTTTTTTTTTTTG
GCCAGAAAACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTCCTTTTTCAATTTTTCG
TTTATTTAAAAAAATTATAAACTCTACT
Found at i:18649 original size:54 final size:55
Alignment explanation
Indices: 18502--18651 Score: 134
Period size: 54 Copynumber: 2.8 Consensus size: 55
18492 TTTCTCTTAA
* * * * * *
18502 AAAAAACTCTATTTTTATTTAATTAAGTCTAATATTCTTACTATTTTATTTTAATT
1 AAAAAACTCTAATTTTATTTTATTAAATCTAATATTTTTA-TATTTTATGTCAATT
* *
18558 AAAAAACT-TAAATATTATAATTT-TTAAA--T-ATACTTTTATAGTTTTA-GTCAATT
1 AAAAAACTCT-AAT-TT-TATTTTATTAAATCTAATATTTTTATA-TTTTATGTCAATT
18611 -AAAAACTCTAATTTTATTTTATTAAATCTAATATTTTTATA
1 AAAAAACTCTAATTTTATTTTATTAAATCTAATATTTTTATA
18652 CCTATTTTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
50 5 0.07
51 7 0.09
52 10 0.13
53 9 0.12
54 22 0.29
55 2 0.03
56 10 0.13
57 6 0.08
58 4 0.05
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (55 bp):
AAAAAACTCTAATTTTATTTTATTAAATCTAATATTTTTATATTTTATGTCAATT
Found at i:23224 original size:20 final size:20
Alignment explanation
Indices: 23199--23238 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
23189 ATTGACAACC
23199 CCATTTTGCTAAAAACCCCA
1 CCATTTTGCTAAAAACCCCA
*
23219 CCATTTTGCTAAAAATCCCA
1 CCATTTTGCTAAAAACCCCA
23239 ATTTATTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (20 bp):
CCATTTTGCTAAAAACCCCA
Found at i:24810 original size:22 final size:22
Alignment explanation
Indices: 24785--24829 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
24775 GCATGTCACG
*
24785 TCGGACACCGTGATAGAATCGT
1 TCGGACACCGTGATAAAATCGT
24807 TCGGACACCGTGATAAAATCGT
1 TCGGACACCGTGATAAAATCGT
24829 T
1 T
24830 TGTTCTACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
TCGGACACCGTGATAAAATCGT
Found at i:24977 original size:18 final size:18
Alignment explanation
Indices: 24954--25014 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
24944 AATACAGTTG
24954 ATAGATCTTAGTATATAT
1 ATAGATCTTAGTATATAT
* *
24972 ATAGATCTTAGTGTGTAT
1 ATAGATCTTAGTATATAT
* *
24990 ATATATATATA-TATATAT
1 ATAGATCT-TAGTATATAT
25008 ATTAGAT
1 A-TAGAT
25015 TAGACTATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 28 0.82
19 6 0.18
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.46
Consensus pattern (18 bp):
ATAGATCTTAGTATATAT
Done.