Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010444.1 Corchorus olitorius cultivar O-4 contig10476, 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: 3753
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Found at i:2859 original size:179 final size:179
Alignment explanation
Indices: 2559--2919 Score: 704
Period size: 179 Copynumber: 2.0 Consensus size: 179
2549 GATTGATATG
2559 AGAAACTAAGTTAGAGGAATCTGAATGGGTCCAGGAGAGATATGACCAACTCAACTTGATTGATG
1 AGAAACTAAGTTAGAGGAATCTGAATGGGTCCAGGAGAGATATGACCAACTCAACTTGATTGATG
2624 AAAGAAGGCTAACGGCTCTGTGCCATGGTCAGATGTACCAAAAAAGGATGGAACGGGCGTTCAAC
66 AAAGAAGGCTAACGGCTCTGTGCCATGGTCAGATGTACCAAAAAAGGATGGAACGGGCGTTCAAC
*
2689 AAAAAAGTACGCCCAAGAGAGTTCAAAGTGGGAGATTTGGTACTAAAAA
131 AAAAAAGTACGCCCAAAAGAGTTCAAAGTGGGAGATTTGGTACTAAAAA
2738 AGAAACTAAGTTAGAGGAATCTGAATGGGTCCAGGAGAGATATGACCAACTCAACTTGATTGATG
1 AGAAACTAAGTTAGAGGAATCTGAATGGGTCCAGGAGAGATATGACCAACTCAACTTGATTGATG
*
2803 AAAGAAGGCTAACGGCTTTGTGCCATGGTCAGATGTACCAAAAAAGGATGGAACGGGCGTTCAAC
66 AAAGAAGGCTAACGGCTCTGTGCCATGGTCAGATGTACCAAAAAAGGATGGAACGGGCGTTCAAC
2868 AAAAAAGTACGCCCAAAAGAGTTCAAAGTGGGAGATTTGGTACTAAAAA
131 AAAAAAGTACGCCCAAAAGAGTTCAAAGTGGGAGATTTGGTACTAAAAA
2917 AGA
1 AGA
2920 TTATACCAGA
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 180 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (179 bp):
AGAAACTAAGTTAGAGGAATCTGAATGGGTCCAGGAGAGATATGACCAACTCAACTTGATTGATG
AAAGAAGGCTAACGGCTCTGTGCCATGGTCAGATGTACCAAAAAAGGATGGAACGGGCGTTCAAC
AAAAAAGTACGCCCAAAAGAGTTCAAAGTGGGAGATTTGGTACTAAAAA
Done.