Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020500.1 Corchorus olitorius cultivar O-4 contig20533, 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: 22586
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:616 original size:21 final size:21
Alignment explanation
Indices: 591--633 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
581 TGTTGGGTTA
591 GAGGAAACAGGTTTGGCTGAG
1 GAGGAAACAGGTTTGGCTGAG
612 GAGGAAACAGGTTTGGCTGAG
1 GAGGAAACAGGTTTGGCTGAG
633 G
1 G
634 CATTCAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.44, T:0.19
Consensus pattern (21 bp):
GAGGAAACAGGTTTGGCTGAG
Found at i:3070 original size:47 final size:47
Alignment explanation
Indices: 3001--3095 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
2991 TTTTTGTAAT
3001 TGGGAGAGTTTAGGAACCGAATTTAAGAGCTGGTCAGTGTGGATACA
1 TGGGAGAGTTTAGGAACCGAATTTAAGAGCTGGTCAGTGTGGATACA
3048 TGGGAGAGTTTAGGAACCGAATTTAAGAGCTGGTCAGTGTGGATACA
1 TGGGAGAGTTTAGGAACCGAATTTAAGAGCTGGTCAGTGTGGATACA
3095 T
1 T
3096 TTATTGTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (47 bp):
TGGGAGAGTTTAGGAACCGAATTTAAGAGCTGGTCAGTGTGGATACA
Found at i:10699 original size:55 final size:55
Alignment explanation
Indices: 10613--10722 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
10603 ACATGACAGG
* *
10613 TGAAAGCATTTAAAATGGATTGTATGAGTTTGTTTTATTTTTCTTTGTGATGAAA
1 TGAAAGCATTTAAAATGGATTGTATGAGTTTGTTTTATTTTTCTCTATGATGAAA
* * *
10668 TGAAAGCATTTAGAATGGATTGTGTGGGTTTGTTTTATTTTTCTCTATGATGAAA
1 TGAAAGCATTTAAAATGGATTGTATGAGTTTGTTTTATTTTTCTCTATGATGAAA
10723 ATTAACAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (55 bp):
TGAAAGCATTTAAAATGGATTGTATGAGTTTGTTTTATTTTTCTCTATGATGAAA
Found at i:12996 original size:14 final size:14
Alignment explanation
Indices: 12966--12996 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12956 TTTGCTTATG
*
12966 AAAGTTATGAAGGA
1 AAAGTTATGAAGAA
12980 AAAGTTATGAAGAA
1 AAAGTTATGAAGAA
12994 AAA
1 AAA
12997 AAACAAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (14 bp):
AAAGTTATGAAGAA
Found at i:14861 original size:2 final size:2
Alignment explanation
Indices: 14854--14895 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
14844 CTCCCTTTTG
14854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14896 TAAGAATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19896 original size:27 final size:27
Alignment explanation
Indices: 19858--19931 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
19848 GTTTCCTTTA
19858 TGGATCCCGATGGTCATGAGACAAAAC
1 TGGATCCCGATGGTCATGAGACAAAAC
* ** *
19885 TGGATCCCGATGGTCGTGAGATGAAAT
1 TGGATCCCGATGGTCATGAGACAAAAC
*
19912 TAGATCCCGATGGTCATGAG
1 TGGATCCCGATGGTCATGAG
19932 CAATTTGGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (27 bp):
TGGATCCCGATGGTCATGAGACAAAAC
Found at i:21096 original size:30 final size:30
Alignment explanation
Indices: 21062--21511 Score: 609
Period size: 30 Copynumber: 14.9 Consensus size: 30
21052 TTTATCATCG
* *
21062 TTATTTTAATCCTGGTTGAGGAT-ATTTGCC
1 TTATTTTAATCCTGTTTGAGGATCA-TTGCT
**
21092 TTATTTTAATGTTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* * **
21122 TTATTTTAATCCTATTTGAGGATTACCGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* **
21152 TTATTTTAATCCTGTTTGAGGATTACCGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* *
21182 TTATTTTAATCCTGTTTGAGGATTACTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
21212 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* *
21242 TTATTTTAATCCTGGTTAAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
21272 TTATGTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* * * *
21302 TTATGTCAATCCTGGTTGAGGATCGTTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
21332 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
21362 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
21392 TTATTTTAATCCTGGTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* * *
21422 TTATGAGTTAATCCTGGTTT-AGAATCGTTGCT
1 TTAT--TTTAATCCT-GTTTGAGGATCATTGCT
*
21454 TTATTTTAATCATGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
21484 TTATTTTAATCCTGGTTT-AGGATCATTG
1 TTATTTTAATCCT-GTTTGAGGATCATTG
21512 TTTCATCAGT
Statistics
Matches: 378, Mismatches: 36, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
29 4 0.01
30 344 0.91
31 5 0.01
32 22 0.06
33 3 0.01
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (30 bp):
TTATTTTAATCCTGTTTGAGGATCATTGCT
Found at i:21812 original size:5 final size:5
Alignment explanation
Indices: 21802--21829 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
21792 TGCTTCGAGT
21802 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
21830 CGGGATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Done.