Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01004081.1 Corchorus olitorius cultivar O-4 contig04094, 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, 732
Length: 1221
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Found at i:350 original size:26 final size:26
Alignment explanation
Indices: 321--395 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
311 TAAATTAAAT
321 TATTAAATCCTAAAGATTTTGGAAAC
1 TATTAAATCCTAAAGATTTTGGAAAC
* *
347 TATTATAT--T-AA-A--TT--AAAT
1 TATTAAATCCTAAAGATTTTGGAAAC
365 TATTAAATCCTAAAGATTTTGGAAAC
1 TATTAAATCCTAAAGATTTTGGAAAC
391 TATTA
1 TATTA
396 TATTGAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
18 10 0.27
20 3 0.08
21 2 0.05
22 2 0.05
23 2 0.05
24 3 0.08
26 15 0.41
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (26 bp):
TATTAAATCCTAAAGATTTTGGAAAC
Found at i:374 original size:44 final size:44
Alignment explanation
Indices: 311--399 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
301 AGGTAAAAAA
311 TAAATTAAATTATTAAATCCTAAAGATTTTGGAAACTATTATAT
1 TAAATTAAATTATTAAATCCTAAAGATTTTGGAAACTATTATAT
355 TAAATTAAATTATTAAATCCTAAAGATTTTGGAAACTATTATAT
1 TAAATTAAATTATTAAATCCTAAAGATTTTGGAAACTATTATAT
399 T
1 T
400 GAATAGAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (44 bp):
TAAATTAAATTATTAAATCCTAAAGATTTTGGAAACTATTATAT
Done.