Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004048.1 Corchorus capsularis cultivar CVL-1 contig04056, 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, 644
Length: 1074
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.29
Found at i:901 original size:117 final size:109
Alignment explanation
Indices: 725--1025 Score: 399
Period size: 117 Copynumber: 2.7 Consensus size: 109
715 TAAATTAAAA
* * *
725 TGGTAAAAATAAA-AAATTATATAAAATATTAAATTTAATTAAATG-AAATAGAGTTTTTAGTAG
1 TGGTAAAAATAAAGTAATTATA-AAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAG
788 AATAAAATTGTATATTAGAAAAAAATTTTTAATATATCCAAAATTTTTTT
65 AATAAAATTGTATATTAGAAAAAAA--TTTAATATATCC-AAA--TTTTT
838 TGGTAAAAAATTAAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGT-AAAAA-T-AAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGT
* *
903 AGAATAAAATTGTATATTAGAAAATAATTTAGTATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAAATTTAATATATCCAAATTTTT
* *
950 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
1015 GTAGAATAAAA
61 GTAGAATAAAA
1026 CTATAATAGT
Statistics
Matches: 171, Mismatches: 7, Indels: 19
0.87 0.04 0.10
Matches are distributed among these distances:
109 28 0.16
110 3 0.02
111 6 0.04
112 9 0.05
113 4 0.02
114 36 0.21
115 12 0.07
116 24 0.14
117 49 0.29
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAAATTTAATATATCCAAATTTTT
Done.