Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021207.1 Corchorus olitorius cultivar O-4 contig21240, 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: 4497
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1552 original size:69 final size:69
Alignment explanation
Indices: 1475--1603 Score: 231
Period size: 69 Copynumber: 1.9 Consensus size: 69
1465 GGTTTAACTC
* *
1475 TATCTCTCAGTCTCTCTTTCAAAAGATTCCAATTGAAGCTTTAAGAAGGAAAAAAAAAAAAAAAC
1 TATCTCTCAGTCTCTCTTCCAAAAGATTCCAAATGAAGCTTTAAGAAGGAAAAAAAAAAAAAAAC
1540 TCTA
66 TCTA
*
1544 TATCTCTCAGTCTCTCTTCCAAAAGATTCTAAATGAAGCTTTAAGAAGGAAAAAAAAAAA
1 TATCTCTCAGTCTCTCTTCCAAAAGATTCCAAATGAAGCTTTAAGAAGGAAAAAAAAAAA
1604 CCCCCAAACT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (69 bp):
TATCTCTCAGTCTCTCTTCCAAAAGATTCCAAATGAAGCTTTAAGAAGGAAAAAAAAAAAAAAAC
TCTA
Found at i:3551 original size:29 final size:30
Alignment explanation
Indices: 3512--3572 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
3502 TATAAATAAT
* *
3512 ATAATACAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
3541 ATAATAAAATTAAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
3571 AT
1 AT
3573 TAAGTAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Done.