Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000607.1 Corchorus olitorius cultivar O-4 contig00607, 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, 679
Length: 1133
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Found at i:668 original size:45 final size:45
Alignment explanation
Indices: 604--699 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
594 TGCATATGCG
*
604 GCAAGGAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
1 GCAAGTAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
649 GCAAGTAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
1 GCAAGTAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
694 GCAAGT
1 GCAAGT
700 TCCAAGCTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.33, C:0.11, G:0.32, T:0.23
Consensus pattern (45 bp):
GCAAGTAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
Found at i:712 original size:21 final size:21
Alignment explanation
Indices: 686--798 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
676 TGCTAGAAGT
686 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
707 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
728 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
749 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
770 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
791 TCATTGGA
1 TCATTGGA
799 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.