Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016366.1 Corchorus capsularis cultivar CVL-1 contig16387, 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: 8664
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Found at i:656 original size:308 final size:309
Alignment explanation
Indices: 98--718 Score: 1235
Period size: 308 Copynumber: 2.0 Consensus size: 309
88 GAGATAAGAA
98 ACGTATTCAAACGGAAAAAGTTTCAAATTATTAAGAACAAAAGTCTCACCAATAATTCATTGATC
1 ACGTATTCAAACGGAAAAAGTTTCAAATTATTAAGAACAAAAGTCTCACCAATAATTCATTGATC
163 GAAAGTACCTAAGGAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGCTTGCAATCCATGAG
66 GAAAGTACCTAAGGAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGCTTGCAATCCATGAG
228 AGACTTACAAGTTTGGAGGCCGGCTGCCTCCTCCCTCTCCTTGGCGGCACAAAACCTAGAAAAAG
131 AGACTTACAAGTTTGGAGGCCGGCTGCCTCCTCCCTCTCCTTGGCGGCACAAAACCTAGAAAAAG
293 ATGTTCTATGCGATACAAGGATTGATTACACCTTGATGTGCTAGGGTTTTAGACTTAAGAGGGTA
196 ATGTTCTATGCGATACAAGGATTGATTACACCTTGATGTGCTAGGGTTTTAGACTTAAGAGGGTA
358 TTTATAGA-GGTGGCTTAGGGATAATTTAGAGCTAAAAAAACCCTAAGG
261 TTTATAGAGGGTGGCTTAGGGATAATTTAGAGCTAAAAAAACCCTAAGG
406 ACGTATTCAAACGGAAAAAGTTTCAAATTATTAAGAACAAAAGTCTCACCAATAATTCATTGATC
1 ACGTATTCAAACGGAAAAAGTTTCAAATTATTAAGAACAAAAGTCTCACCAATAATTCATTGATC
471 GAAAGTACCTAAGGAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGCTTGCAATCCATGAG
66 GAAAGTACCTAAGGAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGCTTGCAATCCATGAG
536 AGACTTACAAGTTTGGAGGCCGGCTGCCTCCTCCCTCTCCTTGGCGGCACAAAACCTAGAAAAAG
131 AGACTTACAAGTTTGGAGGCCGGCTGCCTCCTCCCTCTCCTTGGCGGCACAAAACCTAGAAAAAG
601 ATGTTCTATGCGATACAAGGATTGATTACACCTTGATGTGCTAGGGTTTTAGACTTAAGAGGGTA
196 ATGTTCTATGCGATACAAGGATTGATTACACCTTGATGTGCTAGGGTTTTAGACTTAAGAGGGTA
666 TTTATAGAGGGTGGCTTAGGGATAATTTAGAGCTAAAAAAACCCTAAGG
261 TTTATAGAGGGTGGCTTAGGGATAATTTAGAGCTAAAAAAACCCTAAGG
715 ACGT
1 ACGT
719 GCTGGGCTGC
Statistics
Matches: 312, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
308 268 0.86
309 44 0.14
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (309 bp):
ACGTATTCAAACGGAAAAAGTTTCAAATTATTAAGAACAAAAGTCTCACCAATAATTCATTGATC
GAAAGTACCTAAGGAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGCTTGCAATCCATGAG
AGACTTACAAGTTTGGAGGCCGGCTGCCTCCTCCCTCTCCTTGGCGGCACAAAACCTAGAAAAAG
ATGTTCTATGCGATACAAGGATTGATTACACCTTGATGTGCTAGGGTTTTAGACTTAAGAGGGTA
TTTATAGAGGGTGGCTTAGGGATAATTTAGAGCTAAAAAAACCCTAAGG
Found at i:1189 original size:21 final size:21
Alignment explanation
Indices: 1165--1213 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1155 CAGCTGGGGG
* * *
1165 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
1186 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
1207 CCCATGT
1 CCCATGT
1214 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:3761 original size:26 final size:26
Alignment explanation
Indices: 3727--3783 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
3717 AGAATCTAAC
* *
3727 ATGCAATAAACAATACTAACAAGCAA
1 ATGCTATAAACAATAATAACAAGCAA
*
3753 ATGCTATAAACAATAATAACATGCAA
1 ATGCTATAAACAATAATAACAAGCAA
3779 ATGCT
1 ATGCT
3784 TAACAAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.21
Consensus pattern (26 bp):
ATGCTATAAACAATAATAACAAGCAA
Done.