Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012040.1 Corchorus olitorius cultivar O-4 contig12073, 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: 7430
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:302 original size:3 final size:3
Alignment explanation
Indices: 294--331 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
284 CCACAGGATT
294 TTA TTA TTA GTTA TTA TTA TT- TTA TTA TTA GTTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA T
332 CTGGATACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:309 original size:10 final size:10
Alignment explanation
Indices: 294--331 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
284 CCACAGGATT
294 TTATTATTAG
1 TTATTATTAG
*
304 TTATTATTATT
1 TTATTATTA-G
315 TTATTATTAG
1 TTATTATTAG
325 TTATTAT
1 TTATTAT
332 CTGGATACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (10 bp):
TTATTATTAG
Found at i:315 original size:21 final size:21
Alignment explanation
Indices: 291--331 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
281 AAACCACAGG
291 ATTTTATTATTAGTTATTATT
1 ATTTTATTATTAGTTATTATT
312 ATTTTATTATTAGTTATTAT
1 ATTTTATTATTAGTTATTAT
332 CTGGATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
ATTTTATTATTAGTTATTATT
Found at i:320 original size:11 final size:11
Alignment explanation
Indices: 291--323 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
281 AAACCACAGG
291 ATTTTATTATT
1 ATTTTATTATT
*
302 A-GTTATTATT
1 ATTTTATTATT
312 ATTTTATTATT
1 ATTTTATTATT
323 A
1 A
324 GTTATTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:5552 original size:33 final size:34
Alignment explanation
Indices: 5492--5555 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
5482 TCAAGTTGTT
5492 CCTCCTAATAATTAAGGTTAACAAATTAAATCTA
1 CCTCCTAATAATTAAGGTTAACAAATTAAATCTA
5526 CCTCCTAATAATTAAGG-TAACAAATTAAAT
1 CCTCCTAATAATTAAGGTTAACAAATTAAAT
5556 ATAGGTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (34 bp):
CCTCCTAATAATTAAGGTTAACAAATTAAATCTA
Found at i:7331 original size:13 final size:13
Alignment explanation
Indices: 7313--7354 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
7303 ATCGCGTTTT
7313 TTTTTTTTTAAAA
1 TTTTTTTTTAAAA
**
7326 TTTTTTTTTATTA
1 TTTTTTTTTAAAA
*
7339 -TTTTTTTAAAAA
1 TTTTTTTTTAAAA
7351 TTTT
1 TTTT
7355 CTTTAATTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTAAAA
Found at i:7368 original size:25 final size:25
Alignment explanation
Indices: 7314--7370 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
7304 TCGCGTTTTT
* * *
7314 TTTTTTTTAAAATTTTTTTTTATTA
1 TTTTTTTAAAAATTTTCTTTAATTA
7339 TTTTTTTAAAAATTTTCTTTAATT-
1 TTTTTTTAAAAATTTTCTTTAATTA
*
7363 TCTTTTTA
1 TTTTTTTA
7371 CCCTGTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTTTTAAAAATTTTCTTTAATTA
Done.