Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001850.1 Corchorus capsularis cultivar CVL-1 contig01851, 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, 631
Length: 1053
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Found at i:567 original size:25 final size:25
Alignment explanation
Indices: 539--614 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
529 ATTTCCATTT
539 ATATTAAATTACTTATTAACCAAAG
1 ATATTAAATTACTTATTAACCAAAG
** * ***
564 ATATT---TTAGATATT-TCCATTT
1 ATATTAAATTACTTATTAACCAAAG
*
585 ATATTAAATTTCTTATTAACCAAAG
1 ATATTAAATTACTTATTAACCAAAG
610 ATATT
1 ATATT
615 TTAGATATTT
Statistics
Matches: 34, Mismatches: 13, Indels: 8
0.62 0.24 0.15
Matches are distributed among these distances:
21 8 0.24
22 7 0.21
24 6 0.18
25 13 0.38
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (25 bp):
ATATTAAATTACTTATTAACCAAAG
Found at i:567 original size:46 final size:46
Alignment explanation
Indices: 515--652 Score: 251
Period size: 46 Copynumber: 3.0 Consensus size: 46
505 AAAGTTTAAG
515 AAGATATTTTATG-TATTTCCATTTATATTAAATTACTTATTAACCA
1 AAGATATTTTA-GATATTTCCATTTATATTAAATTACTTATTAACCA
*
561 AAGATATTTTAGATATTTCCATTTATATTAAATTTCTTATTAACCA
1 AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
607 AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
1 AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
653 TTAAAACTTA
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
45 1 0.01
46 88 0.99
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (46 bp):
AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
Done.