Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022010.1 Corchorus olitorius cultivar O-4 contig22043, 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: 21653
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Found at i:246 original size:18 final size:18
Alignment explanation
Indices: 209--281 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
199 AAAGATTTTT
* *
209 TTTATTATTTATTCACTA
1 TTTATTATTTTTTTACTA
*
227 TTTATTATTTTTTTATTA
1 TTTATTATTTTTTTACTA
* *
245 TTGATTTTTTTTTTAAACTA
1 TTTATTATTTTTTT--ACTA
*
265 -TTATCTATTTATTTACT
1 TTTAT-TATTTTTTTACT
282 TTTTTTTCAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
18 30 0.70
19 3 0.07
20 10 0.23
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (18 bp):
TTTATTATTTTTTTACTA
Found at i:287 original size:30 final size:30
Alignment explanation
Indices: 251--311 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
241 ATTATTGATT
*
251 TTTTTTTTAAACTATTATCTATTTATTTAC
1 TTTTTTTTAAACTATTATCTACTTATTTAC
*
281 TTTTTTTTCAACTATTATCTACTTATTTAC
1 TTTTTTTTAAACTATTATCTACTTATTTAC
311 T
1 T
312 ATTTATCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTTTTAAACTATTATCTACTTATTTAC
Found at i:325 original size:19 final size:19
Alignment explanation
Indices: 274--328 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
264 ATTATCTATT
274 TATTTA-CTTTTT-TTTCAAC
1 TATTTATCTTTTTATTT--AC
**
293 TA-TTATCTACTTATTTAC
1 TATTTATCTTTTTATTTAC
311 TATTTATCTTTTTATTTA
1 TATTTATCTTTTTATTTA
329 TTTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 7 0.24
19 19 0.66
20 3 0.10
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTATCTTTTTATTTAC
Found at i:330 original size:4 final size:4
Alignment explanation
Indices: 311--399 Score: 50
Period size: 4 Copynumber: 24.0 Consensus size: 4
301 ACTTATTTAC
* * *
311 TATT TATCT T-TT TATT TA-T T-TT TAAT TA-T TATC TATT TATT TA-A
1 TATT TAT-T TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
* ** *
355 TATT TATT T-TT T-TT TATT AATT TAGC TA-T TATC TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
400 ATTATTATCC
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
3 19 0.29
4 44 0.68
5 2 0.03
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:351 original size:44 final size:43
Alignment explanation
Indices: 270--402 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 43
260 AACTATTATC
* *
270 TATTTATTTACTTT-TTTTTCAACTATTATCTACTTATTTACTATT
1 TATTT-TTTA-TTTATTTTT-AACTATTATCTATTTATTTAATATT
*
315 TATCTTTTTATTTATTTTTAATTATTATCTATTTATTTAATATT
1 TAT-TTTTTATTTATTTTTAACTATTATCTATTTATTTAATATT
* *
359 TATTTTTT-TTTATTAATTTAGCTATTATCTATTTATTTATTATT
1 TATTTTTTATTTATT--TTTAACTATTATCTATTTATTTAATATT
403 ATTATCCTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
42 6 0.08
43 5 0.06
44 53 0.68
45 12 0.15
46 2 0.03
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.66
Consensus pattern (43 bp):
TATTTTTTATTTATTTTTAACTATTATCTATTTATTTAATATT
Found at i:4256 original size:35 final size:35
Alignment explanation
Indices: 4209--4529 Score: 380
Period size: 35 Copynumber: 9.0 Consensus size: 35
4199 TCCAATGCGG
*
4209 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4244 TCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4279 TCCTTTC-AGAAAGTTTT-TATGATCAGAGTTGATC
1 TCATTTCAAG-AAGTTTTCGATGATCAGAGTTGATC
* * *
4313 TCATTTTCAAGATGTTTT-TATGGTCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC
4348 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4383 TCGTTTCAA-AGAGTTTTCGTTGATCAGAGTTGATC
1 TCATTTCAAGA-AGTTTTCGATGATCAGAGTTGATC
** *
4418 TCATTTCAAGAAGTTTTTTATATATGGTCAGAGTTGATC
1 TCATTTCAAGAAG---TTT-TCGATGATCAGAGTTGATC
* * **
4457 TCCTTTCAATAAGTTATTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-T-TTTCGATGATCAGAGTTGATC
4494 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
4529 T
1 T
4530 TCACATTGAT
Statistics
Matches: 248, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
34 33 0.13
35 150 0.60
36 4 0.02
37 30 0.12
38 5 0.02
39 26 0.10
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
Found at i:4390 original size:104 final size:107
Alignment explanation
Indices: 4232--4529 Score: 392
Period size: 104 Copynumber: 2.8 Consensus size: 107
4222 TTTTCGATGA
* * *
4232 TCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATCTCCTTTCAGAAAGTTTT-
1 TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA-AAAGTTTTC
4296 TATGATCAGAGTTGATCTCATTTTCAAG-A-TGTTT-T-TATGG
65 TATGATCAGAGTTGATCTCA-TTTCAAGAAGTGTTTATATATGG
*
4336 TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAAGAGTTTTC
1 TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAA-AGTTTTC
*
4401 GT-TGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATATGG
65 -TATGATCAGAGTTGATCTCATTTCAAGAAG-TGTTTATATATGG
* * **
4445 TCAGAGTTGATCTCCTTTCAATAAGTTATTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTT
1 TCAGAGTTGATCTCATTTCAAGAAG-T-TTTCGATGATCAGAGTTGATCTCATTTCAA-AAGTTT
*
4510 TCGATGATCAGAGTTGATCT
63 TCTATGATCAGAGTTGATCT
4530 TCACATTGAT
Statistics
Matches: 172, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
103 2 0.01
104 65 0.38
105 19 0.11
106 1 0.01
107 4 0.02
108 1 0.01
109 28 0.16
110 1 0.01
111 50 0.29
112 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (107 bp):
TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAAAGTTTTCT
ATGATCAGAGTTGATCTCATTTCAAGAAGTGTTTATATATGG
Found at i:6097 original size:29 final size:30
Alignment explanation
Indices: 6065--6128 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
6055 TATTTTTTTA
*
6065 TTATTGA-TTTTTTTTAAACTATTATCTAT
1 TTATTGACTTTTTTTTAAACTATTATCTAC
* *
6094 TTATTTACTTTTTTTTCAACTATTATCTAC
1 TTATTGACTTTTTTTTAAACTATTATCTAC
6124 TTATT
1 TTATT
6129 TACTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (30 bp):
TTATTGACTTTTTTTTAAACTATTATCTAC
Found at i:6108 original size:30 final size:30
Alignment explanation
Indices: 6072--6132 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
6062 TTATTATTGA
*
6072 TTTTTTTTAAACTATTATCTATTTATTTAC
1 TTTTTTTTAAACTATTATCTACTTATTTAC
*
6102 TTTTTTTTCAACTATTATCTACTTATTTAC
1 TTTTTTTTAAACTATTATCTACTTATTTAC
6132 T
1 T
6133 ATTTATCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTTTTAAACTATTATCTACTTATTTAC
Found at i:6146 original size:19 final size:19
Alignment explanation
Indices: 6095--6149 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
6085 ATTATCTATT
6095 TATTTA-CTTTTT-TTTCAAC
1 TATTTATCTTTTTATTT--AC
**
6114 TA-TTATCTACTTATTTAC
1 TATTTATCTTTTTATTTAC
6132 TATTTATCTTTTTATTTA
1 TATTTATCTTTTTATTTA
6150 TTTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 7 0.24
19 19 0.66
20 3 0.10
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTATCTTTTTATTTAC
Found at i:6151 original size:4 final size:4
Alignment explanation
Indices: 6132--6223 Score: 52
Period size: 4 Copynumber: 24.0 Consensus size: 4
6122 ACTTATTTAC
* * *
6132 TATT TATCT T-TT TATT TA-T T-TT TAAT TA-T TATC TATT TATT TA-A
1 TATT TAT-T TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
* * ** *
6176 TATT TATTT TTTT TATT TATT AATT TAGC TA-T TATC TATT TATT TATT
1 TATT TA-TT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
6224 ATTATTATCC
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
3 13 0.20
4 48 0.73
5 5 0.08
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (4 bp):
TATT
Found at i:6172 original size:44 final size:45
Alignment explanation
Indices: 6097--6226 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 45
6087 TATCTATTTA
* *
6097 TTTACTTT-TTTTTCAACTATTATCTACTTATTTACTATTTA-TCTT
1 TTTA-TTTATTTTT-AACTATTATCTATTTATTTAATATTTATTCTT
* *
6142 TTTATTTATTTTTAATTATTATCTATTTATTTAATATTTATTTTT
1 TTTATTTATTTTTAACTATTATCTATTTATTTAATATTTATTCTT
* *
6187 TTTATTTATTAATTTAGCTATTATCTATTTATTTATTATT
1 TTTATTTATT--TTTAACTATTATCTATTTATTTAATATT
6227 ATTATCCTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 27 0.36
45 22 0.30
47 25 0.34
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.66
Consensus pattern (45 bp):
TTTATTTATTTTTAACTATTATCTATTTATTTAATATTTATTCTT
Found at i:12557 original size:16 final size:17
Alignment explanation
Indices: 12536--12569 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12526 GGCCTTAATT
12536 ATTTTTT-CCTTTATGG
1 ATTTTTTACCTTTATGG
12552 ATTTTTTAGCCTTTATGG
1 ATTTTTTA-CCTTTATGG
12570 GGGTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.59
Consensus pattern (17 bp):
ATTTTTTACCTTTATGG
Found at i:21376 original size:17 final size:17
Alignment explanation
Indices: 21350--21402 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
21340 CATTTTCAAT
*
21350 ATCACCATGGTGATCTA
1 ATCACAATGGTGATCTA
*
21367 ATCACAATGGTGATTTA
1 ATCACAATGGTGATCTA
*
21384 ATCACTAA-GGTGGTCTA
1 ATCAC-AATGGTGATCTA
21401 AT
1 AT
21403 TAACGATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 29 0.94
18 2 0.06
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (17 bp):
ATCACAATGGTGATCTA
Done.