Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001351.1 Corchorus olitorius cultivar O-4 contig01351, 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, 708
Length: 1180
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Found at i:726 original size:179 final size:178
Alignment explanation
Indices: 434--772 Score: 463
Period size: 179 Copynumber: 1.9 Consensus size: 178
424 CCAATTAAGG
* * * *
434 TGATTTAAGTCTCTATTAAAAGATTGTTTCATGATCTACAACTTTTATGAAGGACTCGAAAACTA
1 TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAAAACTA
* ** *
499 AATTTAATGTTTCAAGTATCAAAAATGTTTTCGAAAAATTTATTGTTTC-GCTTAACGGGAAATA
66 AATTTAATGTTTCAAGTATAAAAAATGACTTCCAAAAATTTATTGTTTCAG-TTAAC-GGAAATA
* *
563 GACGGTCTACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGA
129 GACGATCTACTTAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGA
* * * *
613 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCAAAAACTA
1 TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAAAACTA
678 AATTTAATG-TTCAATGTATAAAAAAT-ACTTCCAAAGAA-TTAGTTGTTTCAGTTAACGGAAAT
66 AATTTAATGTTTCAA-GTATAAAAAATGACTTCCAAA-AATTTA-TTGTTTCAGTTAACGGAAAT
740 AGACGATCTACTTAATATTACATAATTTGTGCT
128 AGACGATCTACTTAATATTACATAATTTGTGCT
773 TATGGTGGAA
Statistics
Matches: 141, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
177 3 0.02
178 47 0.33
179 90 0.64
180 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (178 bp):
TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGACTTCCAAAAATTTATTGTTTCAGTTAACGGAAATAGA
CGATCTACTTAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGA
Done.