Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011439.1 Corchorus olitorius cultivar O-4 contig11472, 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: 7947
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Found at i:3093 original size:21 final size:21
Alignment explanation
Indices: 3069--3126 Score: 55
Period size: 23 Copynumber: 2.7 Consensus size: 21
3059 AATCAAGCAT
*
3069 AAAATACCCAAAAAGTATTGG-
1 AAAATACCCAAAAAGT-TGGGC
*
3090 AAAATGACCATAAAAAGTTGGGC
1 AAAAT-ACC-CAAAAAGTTGGGC
*
3113 TAAATACCCAAAAA
1 AAAATACCCAAAAA
3127 AGTCTCTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 10 0.33
22 9 0.30
23 11 0.37
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.17
Consensus pattern (21 bp):
AAAATACCCAAAAAGTTGGGC
Found at i:3283 original size:24 final size:24
Alignment explanation
Indices: 3256--3301 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3246 GTGACTGACG
3256 GCCGTCAGATTTGCTGACGTGGAA
1 GCCGTCAGATTTGCTGACGTGGAA
*
3280 GCCGTCAGATTTGTTGACGTGG
1 GCCGTCAGATTTGCTGACGTGG
3302 CTTTTCCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (24 bp):
GCCGTCAGATTTGCTGACGTGGAA
Found at i:4056 original size:180 final size:177
Alignment explanation
Indices: 3817--4175 Score: 540
Period size: 180 Copynumber: 2.0 Consensus size: 177
3807 TTGACAGTTA
* * * * * *
3817 TACCCTTAATTTTCGATTATATTTCTCAAATGTCATTGTTTAAATTTTTATAGTTTTACTCAACT
1 TACCCTTAATTTTCAAATATATTTCTCAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
**
3882 AAAAACTATATTTTTATTTAATTTAATCTAATATATTTATAAATATTTTATTTTTACCATTTTAC
66 AAAAACTATA-TTTT-TTTAATCAAATCTAATATATTTATAAATATTTTATTTTTACCATTTTAC
3947 TATTTTAATTAAAAAAACTAAGATATATTAGAATTTTTTAAATATATTTCT
129 TATTTTAATT-AAAAAA-TAAGATATATTAGAATTTTTTAAATATATTTCT
* *
3998 TACCCTT-ATTTTCAAATATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAATT
1 TACCCTTAATTTTCAAATATATTTCTCAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
* * *
4062 AAAAACTCTATTTTTTTAATCAAATCTAATATATTTATAACTATTTTATTTTTACTATTTTACTA
66 AAAAACTATATTTTTTTAATCAAATCTAATATATTTATAAATATTTTATTTTTACCATTTTACTA
* *
4127 TTTTAATTTAAAAATTAGATATATTAGAATTTTTTAAATATATTTCT
131 TTTTAATTAAAAAATAAGATATATTAGAATTTTTTAAATATATTTCT
4174 TA
1 TA
4176 AATGACATTA
Statistics
Matches: 163, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
176 34 0.21
177 5 0.03
178 55 0.34
179 4 0.02
180 58 0.36
181 7 0.04
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (177 bp):
TACCCTTAATTTTCAAATATATTTCTCAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
AAAAACTATATTTTTTTAATCAAATCTAATATATTTATAAATATTTTATTTTTACCATTTTACTA
TTTTAATTAAAAAATAAGATATATTAGAATTTTTTAAATATATTTCT
Found at i:4463 original size:32 final size:30
Alignment explanation
Indices: 4420--4516 Score: 104
Period size: 32 Copynumber: 3.1 Consensus size: 30
4410 ACTAAATACT
*
4420 AAAAAAGTCCCTTATGTTTTTCTTTAGAGACA
1 AAAAAAATCCCTTATGTTTTTCTTT-G-GACA
*
4452 AAAAAAATCCCTTATATTTTTCTTTTGGGACA
1 AAAAAAATCCCTTATGTTTTTC-TTT-GGACA
* **
4484 AAAGAAATCGTTTATGTTTTTTCTTTGGACA
1 AAAAAAATCCCTTATG-TTTTTCTTTGGACA
4515 AA
1 AA
4517 TTAGTCCCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
31 7 0.12
32 39 0.70
33 10 0.18
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (30 bp):
AAAAAAATCCCTTATGTTTTTCTTTGGACA
Found at i:4702 original size:29 final size:29
Alignment explanation
Indices: 4659--4733 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
4649 GCTAATTTTT
* *
4659 GAAACGTAAGGGATTAATTTGTCCTGAAAA
1 GAAACATAAGGGATTAATTTGTCC-CAAAA
*
4689 -AAACATAAGGGATTATTTTGTCCCAAAA
1 GAAACATAAGGGATTAATTTGTCCCAAAA
4717 GTGAAACATAAGGGATT
1 --GAAACATAAGGGATT
4734 TTATGGGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.10
29 21 0.54
31 14 0.36
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (29 bp):
GAAACATAAGGGATTAATTTGTCCCAAAA
Found at i:5564 original size:20 final size:20
Alignment explanation
Indices: 5539--5579 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5529 ACTTTAACCC
5539 TATTTTATAAGTATTTGTGT
1 TATTTTATAAGTATTTGTGT
5559 TATTTTATAAGTATTTGTGT
1 TATTTTATAAGTATTTGTGT
5579 T
1 T
5580 TTTAGGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (20 bp):
TATTTTATAAGTATTTGTGT
Found at i:6379 original size:12 final size:13
Alignment explanation
Indices: 6354--6380 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6344 TTTTCATCTA
6354 TTTTTCTAGTTTT
1 TTTTTCTAGTTTT
6367 TTTTTCTAGTTTT
1 TTTTTCTAGTTTT
6380 T
1 T
6381 CCTAAGGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (13 bp):
TTTTTCTAGTTTT
Found at i:7364 original size:3 final size:3
Alignment explanation
Indices: 7356--7408 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
7346 GTTACTAACC
7356 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7404 TTA TT
1 TTA TT
7409 TTAAAAGAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.