Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009221.1 Kokia drynarioides strain JFW-HI SEQ_123926, 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: 2908
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Found at i:458 original size:32 final size:33
Alignment explanation
Indices: 402--472 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
392 ATAAGAAAAA
402 TAAATTCTATTAGGATTTGGAAA-GGAGTAATT
1 TAAATTCTATTAGGATTTGGAAAGGGAGTAATT
* * *
434 TGAATTCTAGTTAGGATTT-TAAAGGGATTAATT
1 TAAATTCTA-TTAGGATTTGGAAAGGGAGTAATT
467 TAAATT
1 TAAATT
473 TCAAATTAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 11 0.33
33 22 0.67
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.41
Consensus pattern (33 bp):
TAAATTCTATTAGGATTTGGAAAGGGAGTAATT
Found at i:2860 original size:30 final size:30
Alignment explanation
Indices: 2826--2899 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
2816 TAACCGGGCA
2826 AGCTTTCTGGAAAGAGCGTTCAGCTGGAAG
1 AGCTTTCTGGAAAGAGCGTTCAGCTGGAAG
*** **
2856 AGCTTTCTGGAAAGCTTGTTCAGCTGGGTG
1 AGCTTTCTGGAAAGAGCGTTCAGCTGGAAG
*
2886 AGCTTTCTAGAAAG
1 AGCTTTCTGGAAAG
2900 CCCGTTTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.28
Consensus pattern (30 bp):
AGCTTTCTGGAAAGAGCGTTCAGCTGGAAG
Done.