Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014815.1 Corchorus olitorius cultivar O-4 contig14848, 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: 4007
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:2759 original size:178 final size:178
Alignment explanation
Indices: 2427--2760 Score: 422
Period size: 178 Copynumber: 1.9 Consensus size: 178
2417 AAACACATAT
*
2427 ATTATATAATATTAAGTAGACCGTCTATTCTCGCGAATCCAAACAACTAATTCTTTGAAAGCATT
1 ATTATATAATATTAAGTAGACCGTCTATTCTCGCGAATCCAAACAACAAATTCTTTGAAAGCATT
* * ** *
2492 TTTTATACCTTGAACATTAAATTTAGTTTTTGAGTCCTTTATGAAAGTTTTAGATCATAAAACAA
66 TTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTCCATGAAAGTTGTAGATCATAAAACAA
*
2557 CCTTTCAAGAAACACTTGAATCACCTCAATCAGACATCTAGAGCAAAA
131 CCTTTCAAGAAACACTTAAATCACCTCAATCAGACATCTAGAGCAAAA
* * * ** * *
2605 ATTATATAATATTAAGTGGACTGTTTATTC-CTGTTAA-CCGAAACAACAAATTTTTTGGAAGCA
1 ATTATATAATATTAAGTAGACCGTCTATTCTC-GCGAATCC-AAACAACAAATTCTTTGAAAGCA
* **
2668 TTTTTGATA-CTTGAAACATTCAATTTAGTTTTCGAGTCCTCCATGAAAGTTGTAGATCATGGAA
64 TTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTCCATGAAAGTTGTAGATCATAAAA
* * * * *
2732 TAATCTTTTAATAGACACTTAAATCACCT
128 CAACCTTTCAAGAAACACTTAAATCACCT
2761 TGATCGGATA
Statistics
Matches: 131, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
177 7 0.05
178 124 0.95
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (178 bp):
ATTATATAATATTAAGTAGACCGTCTATTCTCGCGAATCCAAACAACAAATTCTTTGAAAGCATT
TTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTCCATGAAAGTTGTAGATCATAAAACAA
CCTTTCAAGAAACACTTAAATCACCTCAATCAGACATCTAGAGCAAAA
Found at i:2786 original size:178 final size:177
Alignment explanation
Indices: 2427--2802 Score: 418
Period size: 178 Copynumber: 2.1 Consensus size: 177
2417 AAACACATAT
*
2427 ATTATATAATATTAAGTAGACCGTCTATTCTCGCGAATCCAAACAACTAATTCTTTGAAAGCATT
1 ATTATATAATATTAAGTAGACCGTCTATTCTCGCGAATCCAAACAACAAATTCTTTGAAAGCATT
* * ** *
2492 TTTTATACCTTGAACATTAAATTTAGTTTTTGAGTCCTTTATGAAAGTTTTAGATCATAAAACAA
66 TTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTCCATGAAAGTTGTAGATCATAAAACAA
* *
2557 CCTTTCAAGAAACACTTGAATCACCTCAATCAGACATCTAGAGCAAAA
131 CCTTTCAAGAAACACTTAAATCACCTCAATCAGACAACTAGAG-AAAA
* * * ** * *
2605 ATTATATAATATTAAGTGGACTGTTTATTC-CTGTTAA-CCGAAACAACAAATTTTTTGGAAGCA
1 ATTATATAATATTAAGTAGACCGTCTATTCTC-GCGAATCC-AAACAACAAATTCTTTGAAAGCA
* **
2668 TTTTTGATA-CTTGAAACATTCAATTTAGTTTTCGAGTCCTCCATGAAAGTTGTAGATCATGGAA
64 TTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTCCATGAAAGTTGTAGATCATAAAA
* * * * * ** * *
2732 TAATCTTTTAATAGACACTTAAATCACCTTGATCGGATAACT-GAAGAGAAA
128 CAACCTTTCAAGAAACACTTAAATCACCTCAATCAGACAACTAG-AGA-AAA
*
2783 ATTATATAATATTAAATAGA
1 ATTATATAATATTAAGTAGA
2803 ACGTTAAGCC
Statistics
Matches: 164, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
177 9 0.05
178 155 0.95
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (177 bp):
ATTATATAATATTAAGTAGACCGTCTATTCTCGCGAATCCAAACAACAAATTCTTTGAAAGCATT
TTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTCCATGAAAGTTGTAGATCATAAAACAA
CCTTTCAAGAAACACTTAAATCACCTCAATCAGACAACTAGAGAAAA
Done.