Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015034.1 Corchorus olitorius cultivar O-4 contig15067, 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: 13297
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3849 original size:13 final size:13
Alignment explanation
Indices: 3831--3858 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3821 TCAAAGGATG
3831 TTTAACACACCTC
1 TTTAACACACCTC
3844 TTTAACACACCTC
1 TTTAACACACCTC
3857 TT
1 TT
3859 GAGATCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAACACACCTC
Found at i:6062 original size:69 final size:69
Alignment explanation
Indices: 5987--6306 Score: 478
Period size: 69 Copynumber: 4.6 Consensus size: 69
5977 CCAATGTTTA
* * * *
5987 AACTGACTCGCATGGAAACGAGTTTGACTTATGGAAAAGTCTATATGGCTTGGACGAAACCAAGG
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGACGAAACCAAGG
6052 CTTG
66 CTTG
* * ** * *
6056 AACTGACTCATATGGAAATGAGTTTGGCTTGTGGAAAAGCCTACGTGGCTTGGATGGAACCAAGG
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGACGAAACCAAGG
6121 CTTG
66 CTTG
* *
6125 AACTGACTCGTATGTAAACGAGTTTGGCTTGTGGAAAAGTCTATATGGCTTGGACGAAACCAAGG
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGACGAAACCAAGG
6190 CTTG
66 CTTG
* ** * *
6194 AACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACGTGGCTTGGATGGAACCAAGG
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGACGAAACCAAGG
6259 CTTG
66 CTTG
*
6263 AACTGACTCGTATGCAAACGAGTTTGGCTTGTGGAAAAGCCTAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAT
6307 GTTGATAACT
Statistics
Matches: 223, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 223 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (69 bp):
AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGACGAAACCAAGG
CTTG
Found at i:6129 original size:138 final size:138
Alignment explanation
Indices: 5968--6306 Score: 588
Period size: 138 Copynumber: 2.5 Consensus size: 138
5958 CTCTGTTGTA
* * * * * * *
5968 TGGATGGAACCAATGTTTAAACTGACTCGCATGGAAACGAGTTTGACTTATGGAAAAGTCTATAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGCAAACGAGTTTGGCTTGTGGAAAAGTCTATAT
*
6033 GGCTTGGACGAAACCAAGGCTTGAACTGACTCATATGGAAATGAGTTTGGCTTGTGGAAAAGCCT
66 GGCTTGGACGAAACCAAGGCTTGAACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
6098 ACGTGGCT
131 ACGTGGCT
*
6106 TGGATGGAACCAAGGCTTGAACTGACTCGTATGTAAACGAGTTTGGCTTGTGGAAAAGTCTATAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGCAAACGAGTTTGGCTTGTGGAAAAGTCTATAT
6171 GGCTTGGACGAAACCAAGGCTTGAACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
66 GGCTTGGACGAAACCAAGGCTTGAACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
6236 ACGTGGCT
131 ACGTGGCT
*
6244 TGGATGGAACCAAGGCTTGAACTGACTCGTATGCAAACGAGTTTGGCTTGTGGAAAAGCCTAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGCAAACGAGTTTGGCTTGTGGAAAAGTCTAT
6307 GTTGATAACT
Statistics
Matches: 191, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
138 191 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (138 bp):
TGGATGGAACCAAGGCTTGAACTGACTCGTATGCAAACGAGTTTGGCTTGTGGAAAAGTCTATAT
GGCTTGGACGAAACCAAGGCTTGAACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
ACGTGGCT
Found at i:6319 original size:50 final size:50
Alignment explanation
Indices: 6263--6752 Score: 856
Period size: 50 Copynumber: 9.8 Consensus size: 50
6253 CCAAGGCTTG
*
6263 AACTGACTCGTATGCAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
**
6313 AACTGACTCGTATGGAAACGAGTTTGGCTTGTCAAAAAGCCTATGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
*
6363 AATTGACTCGTATGG-AACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
6412 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
*
6462 AACTGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
* *
6512 AACTGACTCGTATGGAACCGAGTTCGGCTTGTGGAAAAGCCTATGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
6562 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
* *
6612 AATTGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
*
6662 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAAGTTGAT
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
* * *
6712 AATTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
6753 AAAGCATTCG
Statistics
Matches: 420, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
49 46 0.11
50 374 0.89
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (50 bp):
AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
Found at i:7518 original size:50 final size:50
Alignment explanation
Indices: 7423--7518 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
7413 CTTAAATGCC
* * *
7423 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGGATGCAATCCTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCCTA
*
7473 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAAT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAAT
7519 TTTATTGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCCTA
Done.