Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009347.1 Corchorus olitorius cultivar O-4 contig09377, 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, 884
Length: 1474
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Found at i:806 original size:26 final size:26
Alignment explanation
Indices: 770--847 Score: 156
Period size: 26 Copynumber: 3.0 Consensus size: 26
760 AGAGATACGG
770 AATGAATCCTAATCAAATTGTCTTCA
1 AATGAATCCTAATCAAATTGTCTTCA
796 AATGAATCCTAATCAAATTGTCTTCA
1 AATGAATCCTAATCAAATTGTCTTCA
822 AATGAATCCTAATCAAATTGTCTTCA
1 AATGAATCCTAATCAAATTGTCTTCA
848 GTGGGCAGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (26 bp):
AATGAATCCTAATCAAATTGTCTTCA
Found at i:813 original size:15 final size:15
Alignment explanation
Indices: 770--839 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
760 AGAGATACGG
770 AATGAATCCTAATCA
1 AATGAATCCTAATCA
785 AATTG--T-CT--TCA
1 AA-TGAATCCTAATCA
796 AATGAATCCTAATCA
1 AATGAATCCTAATCA
811 AATTG--T-CT--TCA
1 AA-TGAATCCTAATCA
822 AATGAATCCTAATCA
1 AATGAATCCTAATCA
837 AAT
1 AAT
840 TGTCTTCAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 24
0.64 0.00 0.36
Matches are distributed among these distances:
10 4 0.09
11 10 0.23
12 2 0.05
13 8 0.19
14 2 0.05
15 13 0.30
16 4 0.09
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (15 bp):
AATGAATCCTAATCA
Done.