Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000546.1 Corchorus olitorius cultivar O-4 contig00546, 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, 705
Length: 1176
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:547 original size:7 final size:7
Alignment explanation
Indices: 535--588 Score: 92
Period size: 7 Copynumber: 7.7 Consensus size: 7
525 TAAAAAAAAT
535 AATTTGA
1 AATTTGA
542 AATTTGA
1 AATTTGA
549 AATTTGA
1 AATTTGA
556 AATTTGA
1 AATTTGA
563 AATTTGA
1 AATTTGA
570 AATTTGA
1 AATTTGA
577 AATATT-A
1 AAT-TTGA
584 AATTT
1 AATTT
589 TAGTAAAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 2 0.04
7 42 0.91
8 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (7 bp):
AATTTGA
Found at i:727 original size:28 final size:28
Alignment explanation
Indices: 687--743 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
677 CTACCATCCC
687 ACCTCCCCCCATTGTAAAATAAAACGAA
1 ACCTCCCCCCATTGTAAAATAAAACGAA
715 ACCTCCCCCCATTGTAAAATAAAACGAA
1 ACCTCCCCCCATTGTAAAATAAAACGAA
743 A
1 A
744 GAGAGATTAA
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:0.44, C:0.32, G:0.07, T:0.18
Consensus pattern (28 bp):
ACCTCCCCCCATTGTAAAATAAAACGAA
Done.