Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020457.1 Corchorus olitorius cultivar O-4 contig20490, 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: 27054
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:6469 original size:49 final size:47
Alignment explanation
Indices: 6375--6516 Score: 171
Period size: 49 Copynumber: 3.0 Consensus size: 47
6365 GAGCGTGCTA
* *
6375 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCAAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
* *
6422 ATCAATTTTTTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-AAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* *
6471 ATCAATTTTGT-AGCAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGTCA--AAAAATTGAGAAAAAGTGCAATGAAAAATAAA
6517 TGGTTGCTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
47 11 0.14
48 28 0.35
49 42 0.52
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCAAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:20177 original size:15 final size:15
Alignment explanation
Indices: 20157--20193 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
20147 TTATTGATCA
20157 CACCATTGTTATTCG
1 CACCATTGTTATTCG
* *
20172 CACCATTGTTGTTTG
1 CACCATTGTTATTCG
20187 CACCATT
1 CACCATT
20194 CGCCCTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (15 bp):
CACCATTGTTATTCG
Found at i:21269 original size:49 final size:47
Alignment explanation
Indices: 21175--21316 Score: 178
Period size: 49 Copynumber: 3.0 Consensus size: 47
21165 GAGCGTGCCA
* *
21175 ATCAATTTTGTAAAAAAATTGATAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTAAAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
**
21222 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGT-AAAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * *
21271 ATCAATTTTGTAGCAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGTA-AAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
21317 GGGTTGCTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 11 0.13
48 28 0.34
49 43 0.52
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (47 bp):
ATCAATTTTGTAAAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:22586 original size:9 final size:9
Alignment explanation
Indices: 22566--22603 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
22556 TTAATTCATT
22566 TAATTTCC-
1 TAATTTCCA
22574 TAATTTCCA
1 TAATTTCCA
*
22583 TAATTTCCT
1 TAATTTCCA
22592 TAATTTCCA
1 TAATTTCCA
22601 TAA
1 TAA
22604 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATTTCCA
Found at i:22586 original size:17 final size:18
Alignment explanation
Indices: 22566--22603 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
22556 TTAATTCATT
22566 TAATTTCC-TAATTTCCA
1 TAATTTCCTTAATTTCCA
22583 TAATTTCCTTAATTTCCA
1 TAATTTCCTTAATTTCCA
22601 TAA
1 TAA
22604 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTTCCTTAATTTCCA
Found at i:27020 original size:3 final size:3
Alignment explanation
Indices: 27012--27054 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
27002 TACTTACTTA
27012 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.