Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017860.1 Corchorus olitorius cultivar O-4 contig17893, 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: 14545
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:498 original size:20 final size:20
Alignment explanation
Indices: 473--512 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
463 AATAGGGAAG
473 CGATATTAGAAGCGGGAAAA
1 CGATATTAGAAGCGGGAAAA
*
493 CGATATTAGAAGCGTGAAAA
1 CGATATTAGAAGCGGGAAAA
513 GCCCTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.17
Consensus pattern (20 bp):
CGATATTAGAAGCGGGAAAA
Found at i:8701 original size:61 final size:61
Alignment explanation
Indices: 8558--8731 Score: 298
Period size: 61 Copynumber: 2.9 Consensus size: 61
8548 ACCCGCGTTG
* * *
8558 CTGTGTTTGATAGGTGAGTATGCCGATAAGGACGATCAAGATCT-GAACC-TATTGCGTAC
1 CTGTGTTTGATAGGTGAGTATGCCGACAGGGACGACCAAGATCTCGAACCTTATTGCGTAC
8617 CTGTGTTTGATAGGTGAGTATGCCGACAGGGACGACCAAGATCTCGAACCTTATTGCGTAC
1 CTGTGTTTGATAGGTGAGTATGCCGACAGGGACGACCAAGATCTCGAACCTTATTGCGTAC
*
8678 CTGTGTTTGATAGGTGAGTATGCCGACAGAGACGACCAAGATCTCGAACCTTAT
1 CTGTGTTTGATAGGTGAGTATGCCGACAGGGACGACCAAGATCTCGAACCTTAT
8732 ACCTATTTAA
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
59 41 0.38
60 5 0.05
61 63 0.58
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (61 bp):
CTGTGTTTGATAGGTGAGTATGCCGACAGGGACGACCAAGATCTCGAACCTTATTGCGTAC
Done.