Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024860.1 Corchorus olitorius cultivar O-4 contig24893, 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: 14260
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:19 original size:2 final size:2
Alignment explanation
Indices: 13--59 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
3 TTCTTTAAGT
*
13 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53 TA TA TA T
1 TA TA TA T
60 TTAGTAGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:315 original size:16 final size:16
Alignment explanation
Indices: 274--317 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
264 TCAAGCTGTC
*
274 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
* *
290 TCGTGCTCGGGTAATT
1 TCGGGTTCGGGTAATT
306 TCGGGTTCGGGT
1 TCGGGTTCGGGT
318 TCGGGTTCGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.39, T:0.39
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:4192 original size:36 final size:36
Alignment explanation
Indices: 4149--4241 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 36
4139 AAATTTATTG
* *
4149 TGACAACTTTTGGTGT-CAATTTAAAAGATAAAATCA
1 TGACAACTTCTGGT-TCCAATTTAAAAGATAAAACCA
*
4185 TGACAACTTCTGGTTCCAATTTAAAAGGTAAAACCA
1 TGACAACTTCTGGTTCCAATTTAAAAGATAAAACCA
* * *
4221 TGACAATTTCAGGTTTCAATT
1 TGACAACTTCTGGTTCCAATT
4242 GGAGATTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 1 0.02
36 49 0.98
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (36 bp):
TGACAACTTCTGGTTCCAATTTAAAAGATAAAACCA
Found at i:4223 original size:100 final size:102
Alignment explanation
Indices: 4084--4274 Score: 253
Period size: 100 Copynumber: 1.9 Consensus size: 102
4074 AATAGGTTAT
* * *
4084 ATGACAACTTCTTGTGTCAATTTGAAAGGTAAAATCATGACAACTT-G-TCAATTGGAAATTTAT
1 ATGACAACTTCTGGTGTCAATTTAAAAGGTAAAACCATGACAACTTAGTTCAATTGGAAATTTAT
* **
4147 TGTGACAACTTTTGGTGTCAATTTAAAAGATAAAATC
66 TATGACAACTTCAGGTGTCAATTTAAAAGATAAAATC
* *
4184 ATGACAACTTCTGGT-TCCAATTTAAAAGGTAAAACCATGACAATTTCAGGTTTCAATTGGAGAT
1 ATGACAACTTCTGGTGT-CAATTTAAAAGGTAAAACCATGACAACTT-A-G-TTCAATTGGAAAT
4248 TTATTATGACAACTTCAGGTGTCAATT
62 TTATTATGACAACTTCAGGTGTCAATT
4275 GGAAATCTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
99 1 0.01
100 40 0.52
103 1 0.01
105 35 0.45
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (102 bp):
ATGACAACTTCTGGTGTCAATTTAAAAGGTAAAACCATGACAACTTAGTTCAATTGGAAATTTAT
TATGACAACTTCAGGTGTCAATTTAAAAGATAAAATC
Found at i:4265 original size:33 final size:33
Alignment explanation
Indices: 4220--4342 Score: 140
Period size: 33 Copynumber: 3.7 Consensus size: 33
4210 AGGTAAAACC
* *
4220 ATGACAATTTCAGGTTTCAATTGGAGATTTATT
1 ATGACAACTTCAGGTGTCAATTGGAGATTTATT
*
4253 ATGACAACTTCAGGTGTCAATTGGAAATCTT-TT
1 ATGACAACTTCAGGTGTCAATTGGAGAT-TTATT
* * * *
4286 ACGACAACTTCAGGTGTGAATTTAGAGATTTATC
1 ATGACAACTTCAGGTGTCAA-TTGGAGATTTATT
* *
4320 ATGACAACTTCTGATGTCAATTG
1 ATGACAACTTCAGGTGTCAATTG
4343 AAAGATCATG
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
33 49 0.66
34 25 0.34
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.37
Consensus pattern (33 bp):
ATGACAACTTCAGGTGTCAATTGGAGATTTATT
Found at i:4353 original size:30 final size:30
Alignment explanation
Indices: 4317--4437 Score: 156
Period size: 30 Copynumber: 4.0 Consensus size: 30
4307 TTAGAGATTT
4317 ATCATGACAACTTCTGATGTCAATTGAAAG
1 ATCATGACAACTTCTGATGTCAATTGAAAG
* *
4347 ATCATGACAACTTCTGGTGTCAAATGCAAA-
1 ATCATGACAACTTCTGATGTCAATTG-AAAG
* *
4377 ATCATGACAACTTAT-AGTGTCAATTGTAAG
1 ATCATGACAACTTCTGA-TGTCAATTGAAAG
* *
4407 ACCATGACAACTTCTGGTGTCAATTGAAAG
1 ATCATGACAACTTCTGATGTCAATTGAAAG
4437 A
1 A
4438 GTAAAATAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.03
30 72 0.94
31 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (30 bp):
ATCATGACAACTTCTGATGTCAATTGAAAG
Found at i:4398 original size:60 final size:60
Alignment explanation
Indices: 4317--4429 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
4307 TTAGAGATTT
* *
4317 ATCATGACAACTTCTGATGTCAATTGAAAGATCATGACAACTTCTGGTGTCAAATGCAAA
1 ATCATGACAACTTATGATGTCAATTGAAAGACCATGACAACTTCTGGTGTCAAATGCAAA
*
4377 ATCATGACAACTTAT-AGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAA
1 ATCATGACAACTTATGA-TGTCAATTGAAAGACCATGACAACTTCTGGTGTCAA
4430 TTGAAAGAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (60 bp):
ATCATGACAACTTATGATGTCAATTGAAAGACCATGACAACTTCTGGTGTCAAATGCAAA
Found at i:7127 original size:4 final size:4
Alignment explanation
Indices: 7118--7150 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
7108 ATTTTTCCGT
7118 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
7151 GAAGACCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:8140 original size:2 final size:2
Alignment explanation
Indices: 8133--8173 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
8123 AAGGAAAATA
* *
8133 AT AT AT AT AT AT AT GT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8174 ATACATGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9268 original size:13 final size:13
Alignment explanation
Indices: 9250--9279 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9240 GGTTTTACTC
9250 TGATTTATGACTT
1 TGATTTATGACTT
*
9263 TGATTTATGATTT
1 TGATTTATGACTT
9276 TGAT
1 TGAT
9280 ATTAACGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57
Consensus pattern (13 bp):
TGATTTATGACTT
Done.