Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004000.1 Corchorus capsularis cultivar CVL-1 contig04008, 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, 961
Length: 1603
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Found at i:608 original size:75 final size:75
Alignment explanation
Indices: 332--597 Score: 462
Period size: 75 Copynumber: 3.5 Consensus size: 75
322 TTAATATTTT
* *
332 CTAAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTCTTTATTATT-TATTTATTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGA-AAATATTCTCA-ACTTTATTATTAT-TTTATTT
396 CTTAAAATATCTC
63 CTTAAAATATCTC
* *
409 CTAAATCTTCCACAATTTGGCAAGAATTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
474 AAAATATCTC
66 AAAATATCTC
484 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
549 AAAATATCTC
66 AAAATATCTC
559 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTC
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTC
598 CCATTATTAT
Statistics
Matches: 182, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
75 142 0.78
76 12 0.07
77 28 0.15
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (75 bp):
CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
AAAATATCTC
Done.