Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012050.1 Corchorus capsularis cultivar CVL-1 contig12071, 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: 7917
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:569 original size:6 final size:6
Alignment explanation
Indices: 552--629 Score: 59
Period size: 6 Copynumber: 13.0 Consensus size: 6
542 TCAACAGCCG
* * * * *
552 CCGCCG CCGCCA CCGCCA TCACCA CCAG-AA CCGCCA CCTCCA CCGCCA
1 CCGCCA CCGCCA CCGCCA CCGCCA CC-GCCA CCGCCA CCGCCA CCGCCA
* * * *
600 CCACAA CCGCCA CCTCCA CCTCCA CCGCCA
1 CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA
630 TCACCTCCAC
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
5 1 0.02
6 54 0.98
ACGTcount: A:0.22, C:0.62, G:0.12, T:0.05
Consensus pattern (6 bp):
CCGCCA
Found at i:595 original size:30 final size:30
Alignment explanation
Indices: 552--634 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
542 TCAACAGCCG
* *
552 CCGCCGCCGCCACCGCCATCACCACCAG-AA
1 CCGCCACCTCCACCGCCATCACCACC-GCAA
* * *
582 CCGCCACCTCCACCGCCACCACAACCGCCA
1 CCGCCACCTCCACCGCCATCACCACCGCAA
*
612 CCTCCACCTCCACCGCCATCACC
1 CCGCCACCTCCACCGCCATCACC
635 TCCACCCCCA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 1 0.02
30 43 0.98
ACGTcount: A:0.22, C:0.61, G:0.11, T:0.06
Consensus pattern (30 bp):
CCGCCACCTCCACCGCCATCACCACCGCAA
Found at i:600 original size:24 final size:24
Alignment explanation
Indices: 558--625 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
548 GCCGCCGCCG
* * *
558 CCGCCACCGCCATCACCACCAGAA
1 CCGCCACCTCCACCACCACCACAA
*
582 CCGCCACCTCCACCGCCACCACAA
1 CCGCCACCTCCACCACCACCACAA
*
606 CCGCCACCTCCACCTCCACC
1 CCGCCACCTCCACCACCACC
626 GCCATCACCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.24, C:0.62, G:0.09, T:0.06
Consensus pattern (24 bp):
CCGCCACCTCCACCACCACCACAA
Found at i:603 original size:15 final size:15
Alignment explanation
Indices: 585--649 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
575 ACCAGAACCG
585 CCACCTCCACCGCCA
1 CCACCTCCACCGCCA
** * * *
600 CCACAACCGCCACCT
1 CCACCTCCACCGCCA
615 CCACCTCCACCGCCA
1 CCACCTCCACCGCCA
* *
630 TCACCTCCACCCCCA
1 CCACCTCCACCGCCA
645 CCACC
1 CCACC
650 ATCTCCACAG
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.22, C:0.66, G:0.05, T:0.08
Consensus pattern (15 bp):
CCACCTCCACCGCCA
Found at i:634 original size:21 final size:21
Alignment explanation
Indices: 610--652 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
600 CCACAACCGC
* *
610 CACCTCCACCTCCACCGCCAT
1 CACCTCCACCCCCACCACCAT
631 CACCTCCACCCCCACCACCAT
1 CACCTCCACCCCCACCACCAT
652 C
1 C
653 TCCACAGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.65, G:0.02, T:0.12
Consensus pattern (21 bp):
CACCTCCACCCCCACCACCAT
Found at i:640 original size:6 final size:6
Alignment explanation
Indices: 585--657 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
575 ACCAGAACCG
* * * * *
585 CCACCT CCACCG CCACCA CAACCG CCACCT CCACCT CCACCG CCA--T
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
* * *
631 -CACCT CCACCC CCACCA CCATCT CCAC
1 CCACCT CCACCT CCACCT CCACCT CCAC
658 AGTCACCCCA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
3 2 0.04
5 1 0.02
6 48 0.94
ACGTcount: A:0.22, C:0.64, G:0.04, T:0.10
Consensus pattern (6 bp):
CCACCT
Found at i:649 original size:30 final size:30
Alignment explanation
Indices: 561--649 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 30
551 GCCGCCGCCG
** *
561 CCACCGCCATCACCACCAGAACCGCCACCT
1 CCACCGCCATCACCACCACCACCACCACCT
* * * *
591 CCACCGCCACCACAACCGCCACCTCCACCT
1 CCACCGCCATCACCACCACCACCACCACCT
* *
621 CCACCGCCATCACCTCCACCCCCACCACC
1 CCACCGCCATCACCACCACCACCACCACC
650 ATCTCCACAG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.24, C:0.63, G:0.07, T:0.07
Consensus pattern (30 bp):
CCACCGCCATCACCACCACCACCACCACCT
Found at i:933 original size:2 final size:2
Alignment explanation
Indices: 926--969 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
916 TCCTAGAGAC
926 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
968 AT
1 AT
970 GAGGGAAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6070 original size:21 final size:20
Alignment explanation
Indices: 6031--6075 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6021 AATTATCAAT
* *
6031 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
6051 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
6072 TAAA
1 TAAA
6076 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Done.