Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012230.1 Corchorus olitorius cultivar O-4 contig12263, 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: 7422
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:367 original size:37 final size:37
Alignment explanation
Indices: 323--406 Score: 168
Period size: 37 Copynumber: 2.3 Consensus size: 37
313 AAGACAATTT
323 CAAGAATTGAAGAGCATTGAAGAATTATTTCAAGAAG
1 CAAGAATTGAAGAGCATTGAAGAATTATTTCAAGAAG
360 CAAGAATTGAAGAGCATTGAAGAATTATTTCAAGAAG
1 CAAGAATTGAAGAGCATTGAAGAATTATTTCAAGAAG
397 CAAGAATTGA
1 CAAGAATTGA
407 GGATTGAGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.24
Consensus pattern (37 bp):
CAAGAATTGAAGAGCATTGAAGAATTATTTCAAGAAG
Found at i:938 original size:10 final size:11
Alignment explanation
Indices: 913--938 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
903 TCATCTTGTA
913 TTTTTCTCTAG
1 TTTTTCTCTAG
924 TTTTTCTCTAG
1 TTTTTCTCTAG
935 TTTT
1 TTTT
939 AGAAGAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTTCTCTAG
Found at i:6895 original size:161 final size:161
Alignment explanation
Indices: 6630--6929 Score: 566
Period size: 161 Copynumber: 1.9 Consensus size: 161
6620 CATTTTTGGC
6630 CTTCTTTTTCTTCCAATTTAATGAAGAAAAATTTATGAAACCTATCAAGACAAAATAAATTCAAG
1 CTTCTTTTTCTTCCAATTTAATGAAGAAAAATTTATGAAACCTATCAAGACAAAATAAATTCAAG
*
6695 TTAGAAGTTAGAAATTAAAAATAAGAAAATTAAAAACTTAAAATGGAAGATAAATAGGAAATTAA
66 TTAGAAGTTAGAAATTAAAAATAAGAAAATTAAAAACTTAAAATGGAAGATAAAAAGGAAATTAA
6760 AATTATTGGCCTTCTTATTTCAATTTTTTTG
131 AATTATTGGCCTTCTTATTTCAATTTTTTTG
6791 CTTCTTTTTCTTCCAATTTAATGAAGAAAAATTCT-TGAAACCTATCAAGACAAAATAAATTCAA
1 CTTCTTTTTCTTCCAATTTAATGAAGAAAAATT-TATGAAACCTATCAAGACAAAATAAATTCAA
*
6855 GTTAGAATTTAGAAATTAAAAATAAGAAAATTAAAAACTTAAAATGGAAGATAAAAAGGAAATTA
65 GTTAGAAGTTAGAAATTAAAAATAAGAAAATTAAAAACTTAAAATGGAAGATAAAAAGGAAATTA
6920 AAATTATTGG
130 AAATTATTGG
6930 GTTTTCTCCC
Statistics
Matches: 136, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
161 135 0.99
162 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (161 bp):
CTTCTTTTTCTTCCAATTTAATGAAGAAAAATTTATGAAACCTATCAAGACAAAATAAATTCAAG
TTAGAAGTTAGAAATTAAAAATAAGAAAATTAAAAACTTAAAATGGAAGATAAAAAGGAAATTAA
AATTATTGGCCTTCTTATTTCAATTTTTTTG
Done.