Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017296.1 Corchorus olitorius cultivar O-4 contig17329, 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: 6978
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Found at i:5932 original size:350 final size:351
Alignment explanation
Indices: 5281--5964 Score: 987
Period size: 350 Copynumber: 2.0 Consensus size: 351
5271 TCCAAGTCGA
* *
5281 TTTAGGAGAAGATCAATTCTGTCAAGAAATTTCAAGGGCAAAATCATCCACTAGAACTGCAGAAA
1 TTTAGGAGAAAATCAATTCTGTCAAGAAATTTCAAGGGCAAAATCATCCACTAGAAATGCAGAAA
* * * * *
5346 TAGGTCTCGAGGTAAACATAAAATTTTTAGATATTGAAATCCTCTTTCCAACGGTACCTCATTTT
66 TAGGTCTCGAGGTAAACATAAAAGTTGTAGATATTGAAATCCTCTTTCCAAAGATACCTCATTTG
* **
5411 CATTTTTCAGAGCTCTAGATCAAAAGTTATGAATTTTCTTCTGAAACTGCTATTGTGAAGTCCTC
131 CATTTTTCAGAGCTCCAGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTATTGTGAAGTCCTC
* * * * *
5476 TTTTGAATAGGATTTAATAATGTTGCATCAGGGTTGAATCATTATTGCATCATAATTACTGATTG
196 TTTCGAATAGGATTTAACAATATTGCATCAGGGCTGAATCATTACTGCATCATAATTACTGATTG
* ** * *
5541 AACTTGGACTCCTTCTTTGGGCTTCCATATTAATGAATTGGGCCTAAGAATATCAGATTTAGCCT
261 AACTTGGACTCCTTCTTTGGGCTTCCATAGTAACAAATTGGGCCTAAGAATATCAAATTTAGACT
5606 TCAAGACATAAGGCCCTCCAGGCCGG
326 TCAAGACATAAGGCCCTCCAGGCCGG
* * *
5632 TTTAGGAGAAAATCAATTTTGTCCAGAAATTTCAAGGGCAAAATCATCCACT-GAAAATGCAGAG
1 TTTAGGAGAAAATCAATTCTGTCAAGAAATTTCAAGGGCAAAATCATCCACTAG-AAATGCAGAA
* * * *
5696 TTAGGTCTCGA-GTTAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAAAGATACCTCATTT
65 ATAGGTCTCGAGGTAAACATAAAAGTTGTAGATATTGAAATCCTCTTTCCAAAGATACCTCATTT
* * * *
5760 GCATTTTTCTGAGCTCCGGATCAAAATTTATGAATTTTCTTCCAAAACTGCTCTTGTGAAGTCCT
130 GCATTTTTCAGAGCTCCAGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTATTGTGAAGTCCT
* ** *
5825 CTTTCGAATAGGATTTAGCAATATTGCATCAGGGCTGAATCATTACTGTGTCATAATTACTTATT
195 CTTTCGAATAGGATTTAACAATATTGCATCAGGGCTGAATCATTACTGCATCATAATTACTGATT
* **
5890 GGACTTGGACTCCTTCTTTGGGCTTCCACT-GTAACAAATTGGGTTTAAGAATATCAAATTTAGA
260 GAACTTGGACTCCTTCTTTGGGCTTCCA-TAGTAACAAATTGGGCCTAAGAATATCAAATTTAGA
5954 CTTCAAGACAT
324 CTTCAAGACAT
5965 CTGGTTTGGC
Statistics
Matches: 293, Mismatches: 38, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
350 225 0.77
351 68 0.23
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (351 bp):
TTTAGGAGAAAATCAATTCTGTCAAGAAATTTCAAGGGCAAAATCATCCACTAGAAATGCAGAAA
TAGGTCTCGAGGTAAACATAAAAGTTGTAGATATTGAAATCCTCTTTCCAAAGATACCTCATTTG
CATTTTTCAGAGCTCCAGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTATTGTGAAGTCCTC
TTTCGAATAGGATTTAACAATATTGCATCAGGGCTGAATCATTACTGCATCATAATTACTGATTG
AACTTGGACTCCTTCTTTGGGCTTCCATAGTAACAAATTGGGCCTAAGAATATCAAATTTAGACT
TCAAGACATAAGGCCCTCCAGGCCGG
Done.