Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000257.1 Corchorus olitorius cultivar O-4 contig00257, 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, 798
Length: 1331
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Found at i:109 original size:22 final size:22
Alignment explanation
Indices: 81--152 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
71 GGGTCCTAAA
81 TCACCTTCTAATGCATGTATGT
1 TCACCTTCTAATGCATGTATGT
* * *
103 TCACCTTCTAATTCCCTTTATG-
1 TCACCTTCTAA-TGCATGTATGT
125 --A--TTCTAATGCATGTATGT
1 TCACCTTCTAATGCATGTATGT
143 TCACCTTCTA
1 TCACCTTCTA
153 TTTCCCTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
17 7 0.18
18 6 0.16
20 2 0.05
22 16 0.42
23 7 0.18
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (22 bp):
TCACCTTCTAATGCATGTATGT
Found at i:141 original size:40 final size:40
Alignment explanation
Indices: 86--182 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 40
76 CTAAATCACC
86 TTCTAATGCATGTATGTTCACCTTCTAATTCCCTTTATGA
1 TTCTAATGCATGTATGTTCACCTTCTAATTCCCTTTATGA
* *
126 TTCTAATGCATGTATGTTCACCTTCTATTTCCCTTTCTGA
1 TTCTAATGCATGTATGTTCACCTTCTAATTCCCTTTATGA
166 TTCTAATGCATGTATGT
1 TTCTAATGCATGTATGT
183 ATTGTTATCG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (40 bp):
TTCTAATGCATGTATGTTCACCTTCTAATTCCCTTTATGA
Done.