Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012866.1 Corchorus capsularis cultivar CVL-1 contig12887, 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: 9655
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:128 original size:15 final size:14
Alignment explanation
Indices: 108--169 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 14
98 TACTTAGTTT
108 ATTAGTTTATGTTTA
1 ATTAGTTTAT-TTTA
*
123 ATTAG--TA-TCTA
1 ATTAGTTTATTTTA
134 ATTAGTTTATTATTA
1 ATTAGTTTATT-TTA
149 ATTAG--TA-TTTA
1 ATTAGTTTATTTTA
160 ATTAGTTTAT
1 ATTAGTTTAT
170 GATTAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
11 16 0.42
12 1 0.03
13 8 0.21
14 1 0.03
15 12 0.32
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (14 bp):
ATTAGTTTATTTTA
Found at i:138 original size:26 final size:26
Alignment explanation
Indices: 108--175 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
98 TACTTAGTTT
108 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
134 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
160 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
176 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:223 original size:24 final size:24
Alignment explanation
Indices: 184--251 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 24
174 AAAATGAAGG
184 AAAATGAA-TTTGAAGATTTGTTA
1 AAAATGAAGTTTGAAGATTTGTTA
* *
207 AAAATGAAGTTTGAAGAAGTCGTTA
1 AAAATGAAGTTTGAAG-ATTTGTTA
* *
232 GAAATGAAGTTT-AAGGTTTG
1 AAAATGAAGTTTGAAGATTTG
252 AAGGTTGAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 10 0.27
24 10 0.27
25 17 0.46
ACGTcount: A:0.41, C:0.01, G:0.24, T:0.34
Consensus pattern (24 bp):
AAAATGAAGTTTGAAGATTTGTTA
Found at i:355 original size:21 final size:21
Alignment explanation
Indices: 314--357 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
304 CAAAAGTGTA
**
314 AAAAGGGGGGCGGTATTTAGC
1 AAAAGGGGGGCGGTAAATAGC
*
335 AAAATGGGGGCGGTAAATAGC
1 AAAAGGGGGGCGGTAAATAGC
356 AA
1 AA
358 TCCAGAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.39, T:0.16
Consensus pattern (21 bp):
AAAAGGGGGGCGGTAAATAGC
Found at i:6684 original size:15 final size:15
Alignment explanation
Indices: 6664--6694 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6654 TAATTGTGGG
*
6664 TGCTGTTGCTGGTGC
1 TGCTGTTGCTGCTGC
6679 TGCTGTTGCTGCTGC
1 TGCTGTTGCTGCTGC
6694 T
1 T
6695 ACAAGAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.35, T:0.42
Consensus pattern (15 bp):
TGCTGTTGCTGCTGC
Found at i:8064 original size:107 final size:110
Alignment explanation
Indices: 7874--8141 Score: 420
Period size: 107 Copynumber: 2.5 Consensus size: 110
7864 AATTTTTCTA
* ** *
7874 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGTTAAACTTAGTG-AATTAGTTATATAGTATAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATAG-ATAT
*
7938 TTTATTTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
65 TTTATTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
7984 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTT-T-T-G-TAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTATATAGATAT
*
8045 TTTATTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTATTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
*
8091 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTGGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTA
8142 AGGCTAAACT
Statistics
Matches: 149, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
106 20 0.13
107 77 0.52
109 1 0.01
110 28 0.19
111 15 0.10
112 8 0.05
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (110 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATAGATATT
TTATTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
Found at i:8169 original size:1 final size:1
Alignment explanation
Indices: 8165--8195 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
8155 TAAAAAGAAC
*
8165 AAAAATAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8196 GAGAAGACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:8173 original size:15 final size:13
Alignment explanation
Indices: 8153--8194 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
8143 GGCTAAACTT
8153 AATAAAAAGAACAAA
1 AATAAAAA-AA-AAA
8168 AATAAAAAAAAAA
1 AATAAAAAAAAAA
8181 AA-AAAAAAAAAA
1 AATAAAAAAAAAA
8193 AA
1 AA
8195 AGAGAAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.44
13 5 0.19
14 2 0.07
15 8 0.30
ACGTcount: A:0.90, C:0.02, G:0.02, T:0.05
Consensus pattern (13 bp):
AATAAAAAAAAAA
Found at i:9305 original size:42 final size:42
Alignment explanation
Indices: 9241--9408 Score: 293
Period size: 42 Copynumber: 4.0 Consensus size: 42
9231 TACGTAGAAT
* *
9241 AACGTTAACGTGTCGTATTTTGATGACGATTTAAGAAAAATG
1 AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
*
9283 AACGATAACGTGTCGTATTTTGATGACGATTTAAGAAAAATG
1 AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
9325 AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
1 AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
9367 AACGATAACGTGCCGTATTTTGATGACGATTTCAA-AAAAATG
1 AACGATAACGTGCCGTATTTTGATGACGATTT-AAGAAAAATG
9409 CAACTTTTTG
Statistics
Matches: 123, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
42 121 0.98
43 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (42 bp):
AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
Found at i:9520 original size:34 final size:33
Alignment explanation
Indices: 9455--9564 Score: 125
Period size: 34 Copynumber: 3.3 Consensus size: 33
9445 CCACCCCAAG
9455 AGGGCGGCTT-ACCATGGGCAGACCGCCCCACT
1 AGGGCGGCTTCACCATGGGCAGACCGCCCCACT
*
9487 AGGGCGGCTTCACCATTGGGCA-AGCCGCTCCACT
1 AGGGCGGCTTCACCA-TGGGCAGA-CCGCCCCACT
* *** *
9521 AGGGCGGCTTCACTATGAATAGGCCGCCCCACT
1 AGGGCGGCTTCACCATGGGCAGACCGCCCCACT
*
9554 GGGGCGGCTTC
1 AGGGCGGCTTC
9565 GCCACGGCAG
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
32 10 0.15
33 27 0.41
34 29 0.44
ACGTcount: A:0.17, C:0.35, G:0.32, T:0.16
Consensus pattern (33 bp):
AGGGCGGCTTCACCATGGGCAGACCGCCCCACT
Found at i:9553 original size:33 final size:34
Alignment explanation
Indices: 9477--9564 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 34
9467 CATGGGCAGA
**
9477 CCGCCCCACTAGGGCGGCTTCACCATTGGGCAAG
1 CCGCCCCACTAGGGCGGCTTCACCATTGAACAAG
* * * *
9511 CCGCTCCACTAGGGCGGCTTCACTA-TGAATAGG
1 CCGCCCCACTAGGGCGGCTTCACCATTGAACAAG
*
9544 CCGCCCCACTGGGGCGGCTTC
1 CCGCCCCACTAGGGCGGCTTC
9565 GCCACGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
33 23 0.50
34 23 0.50
ACGTcount: A:0.16, C:0.38, G:0.30, T:0.17
Consensus pattern (34 bp):
CCGCCCCACTAGGGCGGCTTCACCATTGAACAAG
Done.