Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000756.1 Corchorus olitorius cultivar O-4 contig00756, 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, 618
Length: 1030
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Found at i:78 original size:33 final size:33
Alignment explanation
Indices: 36--113 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
26 ATTAATTAAG
* * * *
36 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
69 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
102 AAGTTCAAAATC
1 AAGTTCAAAATC
114 CACAATTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:278 original size:7 final size:7
Alignment explanation
Indices: 269--569 Score: 386
Period size: 7 Copynumber: 43.0 Consensus size: 7
259 AATAGTCAAT
*
269 TCAAAAT
1 TCAAAAC
*
276 TCAAAAT
1 TCAAAAC
*
283 TCAAAAT
1 TCAAAAC
*
290 TCAAAAT
1 TCAAAAC
*
297 TCAAAAT
1 TCAAAAC
*
304 TCAAAAT
1 TCAAAAC
*
311 TCAAAAT
1 TCAAAAC
*
318 TCAAAAT
1 TCAAAAC
*
325 TCAAAAT
1 TCAAAAC
*
332 TCAAAAT
1 TCAAAAC
*
339 TCAAAAT
1 TCAAAAC
*
346 TCAAAAT
1 TCAAAAC
*
353 TCAAAAT
1 TCAAAAC
*
360 TCAAAAT
1 TCAAAAC
*
367 TCAAAAT
1 TCAAAAC
*
374 TCAAAAT
1 TCAAAAC
381 TCAAAAC
1 TCAAAAC
388 TCAAAAC
1 TCAAAAC
395 TCAAAAC
1 TCAAAAC
402 TCAAAAC
1 TCAAAAC
409 TCAAAAC
1 TCAAAAC
416 TCAAAAC
1 TCAAAAC
423 TCAAAAC
1 TCAAAAC
430 TCAAAAC
1 TCAAAAC
437 TCAAAAC
1 TCAAAAC
444 TCAAAAC
1 TCAAAAC
451 TCAAAAC
1 TCAAAAC
458 TCAAAAC
1 TCAAAAC
465 TCAAAAC
1 TCAAAAC
472 TCAAAAC
1 TCAAAAC
479 TCAAAAC
1 TCAAAAC
486 TCAAAAC
1 TCAAAAC
493 TCAAAAC
1 TCAAAAC
*
500 TCAAAAG
1 TCAAAAC
507 TCAAAAC
1 TCAAAAC
514 TCAAAAC
1 TCAAAAC
521 TCAAAAC
1 TCAAAAC
*
528 TCAAAAT
1 TCAAAAC
*
535 TCAAAAT
1 TCAAAAC
***
542 TCATGGC
1 TCAAAAC
*
549 TCAAAAA
1 TCAAAAC
*
556 TCAAAAT
1 TCAAAAC
563 TCAAAAC
1 TCAAAAC
570 CTGCATTTCA
Statistics
Matches: 280, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 280 1.00
ACGTcount: A:0.56, C:0.22, G:0.01, T:0.21
Consensus pattern (7 bp):
TCAAAAC
Done.