Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022240.1 Corchorus olitorius cultivar O-4 contig22273, 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: 20296
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Found at i:435 original size:84 final size:84
Alignment explanation
Indices: 302--467 Score: 323
Period size: 84 Copynumber: 2.0 Consensus size: 84
292 GTCATTCGGG
302 TTTTGACTCATCTGGGTTCAGATCATTCGGGTATGCTAGGTCTAAGGTCAGGTGGGTTCGGGTTT
1 TTTTGACTCATCTGGGTTCAGATCATTCGGGTATGCTAGGTCTAAGGTCAGGTGGGTTCGGGTTT
367 TGGTCTCAGGTCACTCGAA
66 TGGTCTCAGGTCACTCGAA
*
386 TTTTGACTCATCTGGGTTCAGATCATTCGGGTATGCTAGGTCTAGGGTCAGGTGGGTTCGGGTTT
1 TTTTGACTCATCTGGGTTCAGATCATTCGGGTATGCTAGGTCTAAGGTCAGGTGGGTTCGGGTTT
451 TGGTCTCAGGTCACTCG
66 TGGTCTCAGGTCACTCG
468 GGTTGGATTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (84 bp):
TTTTGACTCATCTGGGTTCAGATCATTCGGGTATGCTAGGTCTAAGGTCAGGTGGGTTCGGGTTT
TGGTCTCAGGTCACTCGAA
Found at i:1581 original size:12 final size:12
Alignment explanation
Indices: 1564--1590 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1554 AATTTCATCC
1564 ATAGATAATTTG
1 ATAGATAATTTG
1576 ATAGATAATTTG
1 ATAGATAATTTG
1588 ATA
1 ATA
1591 TGTACAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (12 bp):
ATAGATAATTTG
Found at i:2830 original size:37 final size:37
Alignment explanation
Indices: 2789--2863 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2779 TTTGCTATTT
2789 AAAAAATCTGGACAATTTGCAGAAGCACTTTTGTTGC
1 AAAAAATCTGGACAATTTGCAGAAGCACTTTTGTTGC
*
2826 AAAAAATCTGGACAATTTGGAGAAGCACTTTTGTTGC
1 AAAAAATCTGGACAATTTGCAGAAGCACTTTTGTTGC
2863 A
1 A
2864 GCAATGGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (37 bp):
AAAAAATCTGGACAATTTGCAGAAGCACTTTTGTTGC
Found at i:13439 original size:6 final size:7
Alignment explanation
Indices: 13421--13446 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13411 GGAGGCAAGG
13421 GAAAAAT
1 GAAAAAT
13428 GAAAAAT
1 GAAAAAT
13435 GAAAAAT
1 GAAAAAT
13442 GAAAA
1 GAAAA
13447 CGAAGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
GAAAAAT
Found at i:14215 original size:19 final size:20
Alignment explanation
Indices: 14193--14230 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
14183 ATCACATAAA
14193 CGTATAATAA-CGTGTTAGT
1 CGTATAATAATCGTGTTAGT
**
14212 CGTATTTTAATCGTGTTAG
1 CGTATAATAATCGTGTTAG
14231 CTGTGTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (20 bp):
CGTATAATAATCGTGTTAGT
Found at i:14267 original size:18 final size:18
Alignment explanation
Indices: 14240--14278 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
14230 GCTGTGTTTG
* *
14240 ACACGGTTAAGACACGAA
1 ACACGATTAAAACACGAA
*
14258 ACACGATTAAAAGACGAA
1 ACACGATTAAAACACGAA
14276 ACA
1 ACA
14279 TGTTAAGAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.21, G:0.18, T:0.10
Consensus pattern (18 bp):
ACACGATTAAAACACGAA
Done.