Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005558.1 Corchorus capsularis cultivar CVL-1 contig05576, 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: 11331
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4604 original size:28 final size:26
Alignment explanation
Indices: 4573--4633 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
4563 TTATTTTAGA
4573 CAAACTCTTAACCAATTTTAATCTCAAC
1 CAAACTCTT-A-CAATTTTAATCTCAAC
4601 CAAACTC--ACAATTTTAATCTCAAC
1 CAAACTCTTACAATTTTAATCTCAAC
*
4625 CAACCTCTT
1 CAAACTCTT
4634 CAAGATTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 22 0.73
25 1 0.03
28 7 0.23
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (26 bp):
CAAACTCTTACAATTTTAATCTCAAC
Found at i:4740 original size:34 final size:33
Alignment explanation
Indices: 4700--4797 Score: 106
Period size: 39 Copynumber: 2.8 Consensus size: 33
4690 TATCCACTTA
*
4700 ATATAATTGGAATTGGATTAAGAAAACCCGTAAT
1 ATATAATTGGAATTGGATTAA-AAAACCCATAAT
*
4734 ATATAATTTGAATTGGACTAATAAAATTCAACCCATAAT
1 ATATAATTGGAATTGGA-T--TAAAA---AACCCATAAT
*
4773 ATATAATTGGAATTGGACTAAAAAA
1 ATATAATTGGAATTGGATTAAAAAA
4798 ATTCAATTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
33 2 0.04
34 16 0.30
35 1 0.02
36 7 0.13
37 3 0.06
39 25 0.46
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (33 bp):
ATATAATTGGAATTGGATTAAAAAACCCATAAT
Found at i:4773 original size:39 final size:39
Alignment explanation
Indices: 4724--4803 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
4714 GGATTAAGAA
* * *
4724 AACCCGTAATATATAATTTGAATTGGACTAATAAAATTC
1 AACCCATAATATATAATTGGAATTGGACTAAAAAAATTC
4763 AACCCATAATATATAATTGGAATTGGACTAAAAAAATTC
1 AACCCATAATATATAATTGGAATTGGACTAAAAAAATTC
4802 AA
1 AA
4804 TTTGATTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (39 bp):
AACCCATAATATATAATTGGAATTGGACTAAAAAAATTC
Found at i:8757 original size:42 final size:42
Alignment explanation
Indices: 8698--8825 Score: 229
Period size: 42 Copynumber: 3.0 Consensus size: 42
8688 AAGAGTTCAG
*
8698 GGGCTTATTTGGCTGAAATAATAGTTCAGGGGCTTATTTGAC
1 GGGCTTATTTGGCTGAAATAATAGTTCAGGGACTTATTTGAC
8740 GGGCTTATTTGGCTGAAATAATAGTTCAGGGACTTATTTGAC
1 GGGCTTATTTGGCTGAAATAATAGTTCAGGGACTTATTTGAC
* *
8782 GGGCTTATTTGACTGAAATAATAGTTCAGGGTCTTATTTGAC
1 GGGCTTATTTGGCTGAAATAATAGTTCAGGGACTTATTTGAC
8824 GG
1 GG
8826 TTCGGTGTGA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (42 bp):
GGGCTTATTTGGCTGAAATAATAGTTCAGGGACTTATTTGAC
Found at i:11062 original size:3 final size:3
Alignment explanation
Indices: 11054--11082 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
11044 TTTCCTTTAA
11054 TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
11083 CGTTCACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:11304 original size:2 final size:2
Alignment explanation
Indices: 11297--11326 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11287 ACCATCTGAA
11297 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
11327 GATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.