Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004816.1 Corchorus capsularis cultivar CVL-1 contig04834, 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: 4444
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:309 original size:14 final size:14
Alignment explanation
Indices: 292--326 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
282 ACGAGAACTA
292 GAGAGGGAGAAGGG
1 GAGAGGGAGAAGGG
*
306 GAGAAGGAGAAGGG
1 GAGAGGGAGAAGGG
320 GAGAGGG
1 GAGAGGG
327 GAGCGGCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (14 bp):
GAGAGGGAGAAGGG
Found at i:452 original size:62 final size:61
Alignment explanation
Indices: 348--467 Score: 213
Period size: 62 Copynumber: 2.0 Consensus size: 61
338 GTTCCCCTCC
*
348 ATTTCTTATTAAATATTTTATTTAAAAGTAATATCATCCTTACCTTTCATAAAGCCAACTT
1 ATTTCTTATTAAATATTTTATTTAAAAGTAATATAATCCTTACCTTTCATAAAGCCAACTT
*
409 ATTTCTTATTAAATGTTTTATTTTAAAAGTAATATAATCCTTACCTTTCATAAAGCCAA
1 ATTTCTTATTAAATATTTTA-TTTAAAAGTAATATAATCCTTACCTTTCATAAAGCCAA
468 GTCCCCAGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 19 0.34
62 37 0.66
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (61 bp):
ATTTCTTATTAAATATTTTATTTAAAAGTAATATAATCCTTACCTTTCATAAAGCCAACTT
Done.