Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013230.1 Corchorus capsularis cultivar CVL-1 contig13251, 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: 6228
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:3677 original size:14 final size:14
Alignment explanation
Indices: 3660--3686 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3650 CCCAAAAGGC
3660 AAAAAAAAAAAACT
1 AAAAAAAAAAAACT
3674 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
3687 AAAGACCCTC
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:0.89, C:0.07, G:0.00, T:0.04
Consensus pattern (14 bp):
AAAAAAAAAAAACT
Found at i:5201 original size:464 final size:464
Alignment explanation
Indices: 4333--5252 Score: 1813
Period size: 464 Copynumber: 2.0 Consensus size: 464
4323 AGATGGTGAT
4333 GAAAGTTAAAGGTAGGGAATTTGGAAGCATTTGCGTACCTTGCTCGAATAAGGAAATAATTTATT
1 GAAAGTTAAAGGTAGGGAATTTGGAAGCATTTGCGTACCTTGCTCGAATAAGGAAATAATTTATT
*
4398 TGTCATTTTTGAGATGTCTCTATGCATGAACTGAATATATGTGATTTTATATAATGTTTGAGAGG
66 TGTCATTTTTGAGATGTCTCTATGCATGAACTGAATATATGTGATTTTATATAATGTCTGAGAGG
4463 TGATGAAAAAATTTTTCCCTCTCTGCTCCCAAACCACCTCCCAGTCCCATGTCGAGCTGCTCAGT
131 TGATGAAAAAATTTTTCCCTCTCTGCTCCCAAACCACCTCCCAGTCCCATGTCGAGCTGCTCAGT
4528 AGCTTCATGTGCTTACGAGAAGTCAGCGGATGAAAAATACATATGCACGTCAATATGTACTAGTT
196 AGCTTCATGTGCTTACGAGAAGTCAGCGGATGAAAAATACATATGCACGTCAATATGTACTAGTT
4593 TATTGAGAGTGGGACCCGTCAATAGTAACTTTTTCCTAAAGTTCCCAAATACCCTCGAACATCAA
261 TATTGAGAGTGGGACCCGTCAATAGTAACTTTTTCCTAAAGTTCCCAAATACCCTCGAACATCAA
4658 TCGAAATAACAAAAATACCAAGCACAAAAGTACCAAAACACCCTTGACAATTTGTTCTTAGGTGA
326 TCGAAATAACAAAAATACCAAGCACAAAAGTACCAAAACACCCTTGACAATTTGTTCTTAGGTGA
4723 ATGTGATGCAAGATAATGGTTGGTTTTTTGGTCTTTTAACTTCAAACTTTAAGGTGTTGTTTAGA
391 ATGTGATGCAAGATAATGGTTGGTTTTTTGGTCTTTTAACTTCAAACTTTAAGGTGTTGTTTAGA
4788 TATCCTTAG
456 TATCCTTAG
*
4797 GAAAGTTAAAGGTAGGGAATTTGGAAGCATTTGCGTACCTTGCTCGAATAAGGAAATAATTTGTT
1 GAAAGTTAAAGGTAGGGAATTTGGAAGCATTTGCGTACCTTGCTCGAATAAGGAAATAATTTATT
4862 TGTCATTTTTGAGATGTCTCTATGCATGAACTGAATATATGTGATTTTATATAATGTCTGAGAGG
66 TGTCATTTTTGAGATGTCTCTATGCATGAACTGAATATATGTGATTTTATATAATGTCTGAGAGG
4927 TGATGAAAAAATTTTTCCCTCTCTGCTCCCAAACCACCTCCCAGTCCCATGTCGAGCTGCTCAGT
131 TGATGAAAAAATTTTTCCCTCTCTGCTCCCAAACCACCTCCCAGTCCCATGTCGAGCTGCTCAGT
*
4992 AGCTTCCTGTGCTTACGAGAAGTCAGCGGATGAAAAATACATATGCACGTCAATATGTACTAGTT
196 AGCTTCATGTGCTTACGAGAAGTCAGCGGATGAAAAATACATATGCACGTCAATATGTACTAGTT
5057 TATTGAGAGTGGGACCCGTCAATAGTAACTTTTTCCTAAAGTTCCCAAATACCCTCGAACATCAA
261 TATTGAGAGTGGGACCCGTCAATAGTAACTTTTTCCTAAAGTTCCCAAATACCCTCGAACATCAA
5122 TCGAAATAACAAAAATACCAAGCACAAAAGTACCAAAACACCCTTGACAATTTGTTCTTAGGTGA
326 TCGAAATAACAAAAATACCAAGCACAAAAGTACCAAAACACCCTTGACAATTTGTTCTTAGGTGA
5187 ATGTGATGCAAGATAATGGTTGGTTTTTTGGTCTTTTAACTTCAAACTTTAAGGTGTTGTTTAGA
391 ATGTGATGCAAGATAATGGTTGGTTTTTTGGTCTTTTAACTTCAAACTTTAAGGTGTTGTTTAGA
5252 T
456 T
5253 GTTTAGATAT
Statistics
Matches: 453, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
464 453 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (464 bp):
GAAAGTTAAAGGTAGGGAATTTGGAAGCATTTGCGTACCTTGCTCGAATAAGGAAATAATTTATT
TGTCATTTTTGAGATGTCTCTATGCATGAACTGAATATATGTGATTTTATATAATGTCTGAGAGG
TGATGAAAAAATTTTTCCCTCTCTGCTCCCAAACCACCTCCCAGTCCCATGTCGAGCTGCTCAGT
AGCTTCATGTGCTTACGAGAAGTCAGCGGATGAAAAATACATATGCACGTCAATATGTACTAGTT
TATTGAGAGTGGGACCCGTCAATAGTAACTTTTTCCTAAAGTTCCCAAATACCCTCGAACATCAA
TCGAAATAACAAAAATACCAAGCACAAAAGTACCAAAACACCCTTGACAATTTGTTCTTAGGTGA
ATGTGATGCAAGATAATGGTTGGTTTTTTGGTCTTTTAACTTCAAACTTTAAGGTGTTGTTTAGA
TATCCTTAG
Found at i:5607 original size:31 final size:31
Alignment explanation
Indices: 5539--5639 Score: 123
Period size: 31 Copynumber: 3.3 Consensus size: 31
5529 TCCTTTTGTG
* **
5539 CACGTGGCATGCCACGTGCCA-TTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
5569 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * *
5600 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
5631 CATGTGGCA
1 CACGTGGCA
5640 CGACTTTTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 19 0.32
31 41 0.68
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.32
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Done.