Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015246.1 Corchorus capsularis cultivar CVL-1 contig15267, 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: 18851
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Found at i:3749 original size:28 final size:28
Alignment explanation
Indices: 3718--3787 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
3708 ACTAAAAGTT
*
3718 ACCAAAATGTCCCTGAACGTGCAA-AATG
1 ACCAAAATGCCCCTGAA-GTGCAAGAATG
* *
3746 ACCAAAATGCCCCT-TAGTGTAAGAATG
1 ACCAAAATGCCCCTGAAGTGCAAGAATG
3773 ACCAAAATGCCCCTG
1 ACCAAAATGCCCCTG
3788 GACGACCCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 5 0.14
27 19 0.51
28 13 0.35
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (28 bp):
ACCAAAATGCCCCTGAAGTGCAAGAATG
Found at i:3938 original size:12 final size:12
Alignment explanation
Indices: 3917--3956 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3907 GTTGTGGCCG
*
3917 GTTGCCCCATGC
1 GTTGCTCCATGC
3929 GTTGCTCCATGC
1 GTTGCTCCATGC
**
3941 AATGCTCCATGC
1 GTTGCTCCATGC
3953 GTTG
1 GTTG
3957 GCCGGTCATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.12, C:0.33, G:0.25, T:0.30
Consensus pattern (12 bp):
GTTGCTCCATGC
Found at i:6492 original size:6 final size:6
Alignment explanation
Indices: 6479--6516 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
6469 AAAGCAAAAC
6479 AAAT-T AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
6517 GCAGATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:9718 original size:10 final size:10
Alignment explanation
Indices: 9698--9749 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
9688 CGGATGGCAT
9698 GGCATTGGCCG
1 GGCA-TGGCCG
9709 GGCATGGCCG
1 GGCATGGCCG
*
9719 GGCGTGGTGCGCG
1 GGCAT-G-GC-CG
*
9732 GACATGGCCG
1 GGCATGGCCG
9742 GGCATGGC
1 GGCATGGC
9750 TTGGTGTCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 19 0.56
11 7 0.21
12 3 0.09
13 5 0.15
ACGTcount: A:0.10, C:0.27, G:0.50, T:0.13
Consensus pattern (10 bp):
GGCATGGCCG
Found at i:12436 original size:39 final size:41
Alignment explanation
Indices: 12365--12450 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 41
12355 CCCTAAAATT
* * *
12365 AAAAACGGAAAAATATTCTCTTTTTTTATTAGAAAAATCGG
1 AAAAACGGAAAAATATTCTATTTCTTTATTAGAAAAAACGG
12406 AAAAACGGAAAAA-ACTT-TATTTCTTT-TTAGAAAAAACGG
1 AAAAACGGAAAAATA-TTCTATTTCTTTATTAGAAAAAACGG
12445 AAAAAC
1 AAAAAC
12451 AAAAACTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
39 18 0.44
40 8 0.20
41 15 0.37
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (41 bp):
AAAAACGGAAAAATATTCTATTTCTTTATTAGAAAAAACGG
Found at i:12759 original size:12 final size:12
Alignment explanation
Indices: 12737--12769 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12727 AAAAGCAAAA
12737 CAAAT-TAAATC
1 CAAATCTAAATC
*
12748 TAAATCTAAATC
1 CAAATCTAAATC
12760 CAAATCTAAA
1 CAAATCTAAA
12770 GCAGATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (12 bp):
CAAATCTAAATC
Found at i:18089 original size:18 final size:18
Alignment explanation
Indices: 18066--18130 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
18056 CATCGCACAA
18066 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
*
18084 GCCATCGCACGGGC-CAACGCATG
1 GCCAT--C-CGGCCACAAC-C--G
18107 CGCCATCCGGCCACAACCG
1 -GCCATCCGGCCACAACCG
18126 GCCAT
1 GCCAT
18131 TCGATCCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 10 0.27
19 1 0.03
20 5 0.14
21 10 0.27
22 5 0.14
23 1 0.03
24 5 0.14
ACGTcount: A:0.22, C:0.46, G:0.25, T:0.08
Consensus pattern (18 bp):
GCCATCCGGCCACAACCG
Found at i:18093 original size:42 final size:42
Alignment explanation
Indices: 18047--18130 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
18037 CATGGGACGC
*
18047 CGCACGAGACATCGCACAAGCCATCCGGCCACAACCGGCCAT
1 CGCACGAGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
* * ***
18089 CGCACGGGCCAACGCATGCGCCATCCGGCCACAACCGGCCAT
1 CGCACGAGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
18131 TCGATCCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.25, C:0.44, G:0.24, T:0.07
Consensus pattern (42 bp):
CGCACGAGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
Done.