Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021677.1 Corchorus olitorius cultivar O-4 contig21710, 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: 4456
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:3007 original size:47 final size:47
Alignment explanation
Indices: 2938--3034 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
2928 TGTCTACTCA
2938 TTAAATAAACTAAAATATACCAGTACATGCATCATCTGCATTCAGTC
1 TTAAATAAACTAAAATATACCAGTACATGCATCATCTGCATTCAGTC
2985 TTAAATAAACTAAAATATACCAGTACATGCATCATCTGCATTCAGTC
1 TTAAATAAACTAAAATATACCAGTACATGCATCATCTGCATTCAGTC
3032 TTA
1 TTA
3035 CTTTTCTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (47 bp):
TTAAATAAACTAAAATATACCAGTACATGCATCATCTGCATTCAGTC
Found at i:4109 original size:21 final size:21
Alignment explanation
Indices: 4083--4195 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
4073 TGCTAGAAGT
4083 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
4104 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
4125 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
4146 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
4167 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
4188 TCATTGGA
1 TCATTGGA
4196 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.