Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024093.1 Corchorus olitorius cultivar O-4 contig24126, 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, 674
Length: 1124
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Found at i:698 original size:45 final size:45
Alignment explanation
Indices: 634--729 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
624 TGCATATGCG
*
634 GCAAGGAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
1 GCAAGTAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
679 GCAAGTAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
1 GCAAGTAGGCTTGAAGAAGCTTGAAGATGCTAGAAGTTCATTGGA
724 GCAAGT
1 GCAAGT
730 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:742 original size:21 final size:21
Alignment explanation
Indices: 716--828 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
706 TGCTAGAAGT
716 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
737 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
758 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
779 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
800 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
821 TCATTGGA
1 TCATTGGA
829 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.