Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005810.1 Corchorus capsularis cultivar CVL-1 contig05828, 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, 982
Length: 1638
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Found at i:958 original size:27 final size:27
Alignment explanation
Indices: 928--1036 Score: 146
Period size: 27 Copynumber: 4.0 Consensus size: 27
918 TAGTGATTTT
* * *
928 TACTTATACTCATAGCGATGATACCGA
1 TACTTATACTAAAACCGATGATACCGA
* * * * *
955 TACTAATACTAATACCAAGGGTACCGA
1 TACTTATACTAAAACCGATGATACCGA
982 TACTTATACTAAAACCGATGATACCGA
1 TACTTATACTAAAACCGATGATACCGA
1009 TACTTATACTAAAACCGATGATACCGA
1 TACTTATACTAAAACCGATGATACCGA
1036 T
1 T
1037 GAGACCGATG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.27
Consensus pattern (27 bp):
TACTTATACTAAAACCGATGATACCGA
Found at i:1036 original size:9 final size:9
Alignment explanation
Indices: 1022--1065 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
1012 TTATACTAAA
1022 ACCGATGAT
1 ACCGATGAT
*
1031 ACCGATGAG
1 ACCGATGAT
1040 ACCGATGAT
1 ACCGATGAT
1049 ACCGATGAT
1 ACCGATGAT
*
1058 ACCAATGA
1 ACCGATGA
1066 GCCTAAGGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (9 bp):
ACCGATGAT
Done.