Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015220.1 Corchorus capsularis cultivar CVL-1 contig15241, 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: 6652
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Found at i:753 original size:21 final size:21
Alignment explanation
Indices: 727--776 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
717 GAAGAAGAAA
* *
727 AAGAAGAAAGTGAGAACGAGG
1 AAGAAGAAAGTGAAAAAGAGG
*
748 AAGAAGGAAGTGAAAAAGAGG
1 AAGAAGAAAGTGAAAAAGAGG
769 AAGAAGAA
1 AAGAAGAA
777 GGAGCTGCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.36, T:0.04
Consensus pattern (21 bp):
AAGAAGAAAGTGAAAAAGAGG
Found at i:806 original size:18 final size:18
Alignment explanation
Indices: 768--806 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
758 TGAAAAAGAG
* *
768 GAAGAAGAAGGAGCTGCT
1 GAAGAAGAAGAAGCTGAT
*
786 GAAGAAGAAGAATCTGAT
1 GAAGAAGAAGAAGCTGAT
804 GAA
1 GAA
807 AAGGTTGATG
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:0.46, C:0.08, G:0.33, T:0.13
Consensus pattern (18 bp):
GAAGAAGAAGAAGCTGAT
Found at i:1618 original size:12 final size:12
Alignment explanation
Indices: 1601--1626 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1591 CGCTTTAAGG
1601 AGACTACTTTTC
1 AGACTACTTTTC
1613 AGACTACTTTTC
1 AGACTACTTTTC
1625 AG
1 AG
1627 CATGTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (12 bp):
AGACTACTTTTC
Found at i:3972 original size:74 final size:74
Alignment explanation
Indices: 3851--4008 Score: 316
Period size: 74 Copynumber: 2.1 Consensus size: 74
3841 GTGTCCCACC
3851 GGGCGTGCCAAAAAGAGATGTTGCGTCGAAAATCTCTTTGAGAGTTTTCGCGATAAAAACTAAAT
1 GGGCGTGCCAAAAAGAGATGTTGCGTCGAAAATCTCTTTGAGAGTTTTCGCGATAAAAACTAAAT
3916 GACAGTGCA
66 GACAGTGCA
3925 GGGCGTGCCAAAAAGAGATGTTGCGTCGAAAATCTCTTTGAGAGTTTTCGCGATAAAAACTAAAT
1 GGGCGTGCCAAAAAGAGATGTTGCGTCGAAAATCTCTTTGAGAGTTTTCGCGATAAAAACTAAAT
3990 GACAGTGCA
66 GACAGTGCA
3999 GGGCGTGCCA
1 GGGCGTGCCA
4009 GTCAATTTGC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 84 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.23
Consensus pattern (74 bp):
GGGCGTGCCAAAAAGAGATGTTGCGTCGAAAATCTCTTTGAGAGTTTTCGCGATAAAAACTAAAT
GACAGTGCA
Found at i:5679 original size:19 final size:19
Alignment explanation
Indices: 5640--5680 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5630 CCTTGATAAT
*
5640 AATAATAATTATTATTGAA
1 AATAATAATTATTACTGAA
5659 AATAATAATTATTTACT-AA
1 AATAATAATTA-TTACTGAA
5678 AAT
1 AAT
5681 TCGGTCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AATAATAATTATTACTGAA
Done.