Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015356.1 Corchorus olitorius cultivar O-4 contig15389, 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: 17771
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4234 original size:8 final size:7
Alignment explanation
Indices: 4205--4231 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4195 GTAAGATCCA
4205 ATAAAAC
1 ATAAAAC
4212 ATAAAAC
1 ATAAAAC
4219 ATAAAAC
1 ATAAAAC
4226 ATAAAA
1 ATAAAA
4232 ACAAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAC
Found at i:5062 original size:18 final size:18
Alignment explanation
Indices: 5023--5063 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
5013 GTAAAGATTC
* *
5023 GAAAATTTCAAAATCCAT
1 GAAAATTTCAAAATCAAG
5041 GAAAATTTCAAAATCAAG
1 GAAAATTTCAAAATCAAG
5059 GAAAA
1 GAAAA
5064 GTCAACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (18 bp):
GAAAATTTCAAAATCAAG
Found at i:9918 original size:21 final size:20
Alignment explanation
Indices: 9898--9948 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
9888 TGGCCCCCCA
9898 AGCCGCAAGCCTGAGCACCC
1 AGCCGCAAGCCTGAGCACCC
* *
9918 AGCCCGTAGGCCTGAGCACCC
1 AG-CCGCAAGCCTGAGCACCC
*
9939 AGGCGCAAGC
1 AGCCGCAAGC
9949 TGCTGAAGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.24, C:0.41, G:0.29, T:0.06
Consensus pattern (20 bp):
AGCCGCAAGCCTGAGCACCC
Found at i:13809 original size:31 final size:31
Alignment explanation
Indices: 13774--13832 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
13764 ATCATTTTGG
13774 GATCTTGGACTTTTGGGCTTGCATTTGGACA
1 GATCTTGGACTTTTGGGCTTGCATTTGGACA
13805 GATCTTGGACTTTTGGGCTTGCATTTGG
1 GATCTTGGACTTTTGGGCTTGCATTTGG
13833 GCATTCGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.14, C:0.15, G:0.31, T:0.41
Consensus pattern (31 bp):
GATCTTGGACTTTTGGGCTTGCATTTGGACA
Found at i:14615 original size:12 final size:12
Alignment explanation
Indices: 14598--14625 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14588 GTAAGCATTG
14598 CATTTAATTACT
1 CATTTAATTACT
14610 CATTTAATTACT
1 CATTTAATTACT
14622 CATT
1 CATT
14626 CCAAAGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (12 bp):
CATTTAATTACT
Found at i:16302 original size:18 final size:19
Alignment explanation
Indices: 16246--16336 Score: 102
Period size: 18 Copynumber: 4.9 Consensus size: 19
16236 TTGGGTACCT
16246 TTTATGATTTTGGGCTTTTA
1 TTTATGA-TTTGGGCTTTTA
* *
16266 TTT-TAATTT-GGC-ATTA
1 TTTATGATTTGGGCTTTTA
16282 TTTATGATTTGGGC-TTTA
1 TTTATGATTTGGGCTTTTA
*
16300 TTTATGATTTGAGCTTTTA
1 TTTATGATTTGGGCTTTTA
16319 TTTATGCATTTGGG-TTTT
1 TTTATG-ATTTGGGCTTTT
16337 TTGTGTTGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.10
17 8 0.13
18 22 0.36
19 16 0.26
20 9 0.15
ACGTcount: A:0.18, C:0.05, G:0.19, T:0.58
Consensus pattern (19 bp):
TTTATGATTTGGGCTTTTA
Found at i:16967 original size:13 final size:13
Alignment explanation
Indices: 16949--16983 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
16939 TAATTGGAAT
16949 TGCATTCATCATA
1 TGCATTCATCATA
16962 TGCATTCATCATA
1 TGCATTCATCATA
16975 TGCATTCAT
1 TGCATTCAT
16984 GCATTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.40
Consensus pattern (13 bp):
TGCATTCATCATA
Done.