Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001895.1 Corchorus capsularis cultivar CVL-1 contig01897, 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: 1734
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Found at i:692 original size:18 final size:18
Alignment explanation
Indices: 669--720 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
659 TTGAAGGTGA
* *
669 ACCCGATCCCGATCCCGG
1 ACCCGAACCCGAACCCGG
687 ACCCGAACCCGAACCC-G
1 ACCCGAACCCGAACCCGG
* *
704 ATCCGAGCCCGAACCCG
1 ACCCGAACCCGAACCCG
721 AAAATACCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.23, C:0.50, G:0.21, T:0.06
Consensus pattern (18 bp):
ACCCGAACCCGAACCCGG
Found at i:703 original size:24 final size:23
Alignment explanation
Indices: 667--722 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
657 TATTGAAGGT
*
667 GAACCCGATCCCGATCCCG-GACCC
1 GAACCCGAACCCGAT-CCGAG-CCC
691 GAACCCGAACCCGATCCGAGCCC
1 GAACCCGAACCCGATCCGAGCCC
714 GAACCCGAA
1 GAACCCGAA
723 AATACCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.27, C:0.46, G:0.21, T:0.05
Consensus pattern (23 bp):
GAACCCGAACCCGATCCGAGCCC
Found at i:732 original size:16 final size:16
Alignment explanation
Indices: 711--830 Score: 192
Period size: 16 Copynumber: 7.6 Consensus size: 16
701 CCGATCCGAG
711 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
727 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
*
742 CCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATA
758 CCCGAACCCGAAAA-A
1 CCCGAACCCGAAAATA
773 TCCCGAACCCGAAAATA
1 -CCCGAACCCGAAAATA
790 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
806 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
821 CCCGAACCCG
1 CCCGAACCCG
831 CCCAATTGCC
Statistics
Matches: 99, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
15 30 0.30
16 68 0.69
17 1 0.01
ACGTcount: A:0.41, C:0.40, G:0.14, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:748 original size:48 final size:47
Alignment explanation
Indices: 711--830 Score: 183
Period size: 47 Copynumber: 2.6 Consensus size: 47
701 CCGATCCGAG
711 CCCGAACCCGAAAATACCCGAACCCG-AAATACCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATACCCGAACCCGAAAATACCCGAACCCG-AAAAA
758 CCCGAACCCGAAAA-ATCCCGAACCCGAAAATACCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA-CCCGAACCCGAAAATACCCGAACCCGAAAA-A
*
806 CCCGAACCCG-AAGTACCCGAACCCG
1 CCCGAACCCGAAAATACCCGAACCCG
831 CCCAATTGCC
Statistics
Matches: 68, Mismatches: 1, Indels: 8
0.88 0.01 0.10
Matches are distributed among these distances:
46 1 0.01
47 40 0.59
48 27 0.40
ACGTcount: A:0.41, C:0.40, G:0.14, T:0.05
Consensus pattern (47 bp):
CCCGAACCCGAAAATACCCGAACCCGAAAATACCCGAACCCGAAAAA
Found at i:749 original size:31 final size:31
Alignment explanation
Indices: 711--830 Score: 188
Period size: 31 Copynumber: 3.8 Consensus size: 31
701 CCGATCCGAG
711 CCCGAACCCGAAAATACCCGAACCCGAAATA
1 CCCGAACCCGAAAATACCCGAACCCGAAATA
* *
742 CCCGAACCCGAAAAAACCCGAACCCGAAAAA
1 CCCGAACCCGAAAATACCCGAACCCGAAATA
773 TCCCGAACCCGAAAATACCCGAACCCGAAAATA
1 -CCCGAACCCGAAAATACCCGAACCCG-AAATA
*
806 CCCGAACCCG-AAGTACCCGAACCCG
1 CCCGAACCCGAAAATACCCGAACCCG
831 CCCAATTGCC
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
31 43 0.52
32 35 0.43
33 4 0.05
ACGTcount: A:0.41, C:0.40, G:0.14, T:0.05
Consensus pattern (31 bp):
CCCGAACCCGAAAATACCCGAACCCGAAATA
Found at i:769 original size:6 final size:6
Alignment explanation
Indices: 667--722 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
657 TATTGAAGGT
* * * * *
667 GAACCC GATCCC GATCCC GGACCC GAACCC GAACCC G-ATCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
714 GAACCC GAA
1 GAACCC GAA
723 AATACCCGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
5 4 0.10
6 37 0.90
ACGTcount: A:0.27, C:0.46, G:0.21, T:0.05
Consensus pattern (6 bp):
GAACCC
Found at i:1563 original size:21 final size:21
Alignment explanation
Indices: 1530--1574 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1520 TTATAAGGGG
**
1530 TTTGCTATTTACCACCCCCCT
1 TTTGCTAAATACCACCCCCCT
* *
1551 TTTGCTAAATACCGCCTCCCT
1 TTTGCTAAATACCACCCCCCT
1572 TTT
1 TTT
1575 TATAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.38, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTGCTAAATACCACCCCCCT
Done.