Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015506.1 Corchorus capsularis cultivar CVL-1 contig15527, 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: 9307
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--27 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
28 ACACCAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5759 original size:16 final size:16
Alignment explanation
Indices: 5738--5776 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5728 TCCGAGCCCG
*
5738 AACCCGAAAATACTCA
1 AACCCGAAAATACCCA
*
5754 AACCCG-AAATACCCG
1 AACCCGAAAATACCCA
5769 AACCCGAA
1 AACCCGAA
5777 CCCGCCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.46, C:0.36, G:0.10, T:0.08
Consensus pattern (16 bp):
AACCCGAAAATACCCA
Found at i:5960 original size:16 final size:16
Alignment explanation
Indices: 5941--6038 Score: 106
Period size: 16 Copynumber: 6.1 Consensus size: 16
5931 GAACCCGCCT
* *
5941 AAACCTGAACCTGAAA
1 AAACCCGAACCCGAAA
5957 AAACCCGAACCCGAAA
1 AAACCCGAACCCGAAA
** * *
5973 ATGCTCAAACCCGAAA
1 AAACCCGAACCCGAAA
*
5989 AAACACGAACCCGAAA
1 AAACCCGAACCCGAAA
* * *
6005 AAGCTCAAACCCGAAA
1 AAACCCGAACCCGAAA
6021 AAACCCGAACCCGAAA
1 AAACCCGAACCCGAAA
6037 AA
1 AA
6039 GCTCAAACCC
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 66 1.00
ACGTcount: A:0.51, C:0.32, G:0.12, T:0.05
Consensus pattern (16 bp):
AAACCCGAACCCGAAA
Found at i:5989 original size:32 final size:32
Alignment explanation
Indices: 5948--6051 Score: 181
Period size: 32 Copynumber: 3.2 Consensus size: 32
5938 CCTAAACCTG
* *
5948 AACCTGAAAAAACCCGAACCCGAAAATGCTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
*
5980 AACCCGAAAAAACACGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
6012 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
6044 AACCCGAA
1 AACCCGAA
6052 TCCGAAAATT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.50, C:0.33, G:0.12, T:0.05
Consensus pattern (32 bp):
AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
Found at i:6047 original size:16 final size:16
Alignment explanation
Indices: 5964--6051 Score: 113
Period size: 16 Copynumber: 5.5 Consensus size: 16
5954 AAAAAACCCG
*
5964 AACCCGAAAATGCTCA
1 AACCCGAAAAAGCTCA
* * *
5980 AACCCGAAAAAACACG
1 AACCCGAAAAAGCTCA
5996 AACCCGAAAAAGCTCA
1 AACCCGAAAAAGCTCA
* * *
6012 AACCCGAAAAAACCCG
1 AACCCGAAAAAGCTCA
6028 AACCCGAAAAAGCTCA
1 AACCCGAAAAAGCTCA
6044 AACCCGAA
1 AACCCGAA
6052 TCCGAAAATT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.50, C:0.33, G:0.12, T:0.05
Consensus pattern (16 bp):
AACCCGAAAAAGCTCA
Found at i:6280 original size:31 final size:32
Alignment explanation
Indices: 6210--6311 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 32
6200 CAAACAGAAC
* *
6210 CCGAATCCGAATTAACCTGATCCAAATTCAAT
1 CCGAACCCGAATTAACCTGATCCAAATTCAAG
*
6242 CCGAACCCGAATTAACCTGACCCAAATT-AAG
1 CCGAACCCGAATTAACCTGATCCAAATTCAAG
* * *
6273 CCGAACCCGAATTAACCTTATCCAAATCCAAT
1 CCGAACCCGAATTAACCTGATCCAAATTCAAG
6305 CCGAACC
1 CCGAACC
6312 TGACTCAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 27 0.44
32 35 0.56
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.20
Consensus pattern (32 bp):
CCGAACCCGAATTAACCTGATCCAAATTCAAG
Found at i:6285 original size:16 final size:15
Alignment explanation
Indices: 6210--6289 Score: 65
Period size: 15 Copynumber: 5.1 Consensus size: 15
6200 CAAACAGAAC
*
6210 CCGAATCCGAATTAA
1 CCGAACCCGAATTAA
* *
6225 CCTG-ATCCAAATTCAA
1 CC-GAACCCGAATT-AA
6241 TCCGAACCCGAATTAA
1 -CCGAACCCGAATTAA
*
6257 CCTG-ACCCAAATTAA
1 CC-GAACCCGAATTAA
6272 GCCGAACCCGAATTAA
1 -CCGAACCCGAATTAA
6288 CC
1 CC
6290 TTATCCAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
15 25 0.47
16 19 0.36
17 9 0.17
ACGTcount: A:0.38, C:0.33, G:0.11, T:0.19
Consensus pattern (15 bp):
CCGAACCCGAATTAA
Found at i:6352 original size:14 final size:14
Alignment explanation
Indices: 6333--6359 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6323 CGAACCCAAA
6333 AATAACCCGAACCT
1 AATAACCCGAACCT
6347 AATAACCCGAACC
1 AATAACCCGAACC
6360 CGAACCCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.37, G:0.07, T:0.11
Consensus pattern (14 bp):
AATAACCCGAACCT
Found at i:6807 original size:10 final size:10
Alignment explanation
Indices: 6792--6818 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6782 AGGATATCTA
6792 TATCTATATC
1 TATCTATATC
6802 TATCTATATC
1 TATCTATATC
6812 TATCTAT
1 TATCTAT
6819 TTATACTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (10 bp):
TATCTATATC
Done.