Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014987.1 Corchorus olitorius cultivar O-4 contig15020, 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, 948
Length: 1580
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Found at i:458 original size:28 final size:28
Alignment explanation
Indices: 418--474 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
408 GTAATCTCTC
418 TTTCGTTTTATTTTACAATGGGGGGAGG
1 TTTCGTTTTATTTTACAATGGGGGGAGG
446 TTTCGTTTTATTTTACAATGGGGGGAGG
1 TTTCGTTTTATTTTACAATGGGGGGAGG
474 T
1 T
475 GGGATGGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.07, G:0.32, T:0.44
Consensus pattern (28 bp):
TTTCGTTTTATTTTACAATGGGGGGAGG
Found at i:708 original size:7 final size:7
Alignment explanation
Indices: 573--689 Score: 218
Period size: 7 Copynumber: 16.7 Consensus size: 7
563 TCTTTTACTA
573 AAATTT-
1 AAATTTC
579 AATATTTC
1 AA-ATTTC
587 AAATTTC
1 AAATTTC
594 AAATTTC
1 AAATTTC
601 AAATTTC
1 AAATTTC
608 AAATTTC
1 AAATTTC
615 AAATTTC
1 AAATTTC
622 AAATTTC
1 AAATTTC
629 AAATTTC
1 AAATTTC
636 AAATTTC
1 AAATTTC
643 AAATTTC
1 AAATTTC
650 AAATTTC
1 AAATTTC
657 AAATTTC
1 AAATTTC
664 AAATTTC
1 AAATTTC
671 AAATTTC
1 AAATTTC
678 AAATTTC
1 AAATTTC
685 AAATT
1 AAATT
690 ATTTTTTAAA
Statistics
Matches: 109, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
6 2 0.02
7 105 0.96
8 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTC
Done.