Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000420.1 Corchorus olitorius cultivar O-4 contig00420, 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, 631
Length: 1053
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.30
Found at i:371 original size:85 final size:85
Alignment explanation
Indices: 280--438 Score: 291
Period size: 85 Copynumber: 1.9 Consensus size: 85
270 TAATATCATG
*
280 AAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAA
1 AAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGACTAAA
345 ACTATAAAAGTAAAATGGTA
66 ACTATAAAAGTAAAATGGTA
* *
365 AAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTAAA
1 AAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGACTAAA
430 ACTATAAAA
66 ACTATAAAA
439 ATTTAAACAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.33
Consensus pattern (85 bp):
AAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGACTAAA
ACTATAAAAGTAAAATGGTA
Found at i:511 original size:31 final size:31
Alignment explanation
Indices: 476--535 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
466 ATTCATAAAT
*
476 TAAGGGTATAATAGGTGATTCAAAAGTTTGA
1 TAAGGATATAATAGGTGATTCAAAAGTTTGA
*
507 TAAGGATATAATAGGTGATTTAAAAGTTT
1 TAAGGATATAATAGGTGATTCAAAAGTTT
536 TACAAAACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (31 bp):
TAAGGATATAATAGGTGATTCAAAAGTTTGA
Done.