Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008168.1 Kokia drynarioides strain JFW-HI SEQ_122827, 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: 4477
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Found at i:2486 original size:60 final size:60
Alignment explanation
Indices: 2404--2525 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
2394 AGTCTAGTTG
* **
2404 TCCTAAACACTTTCGAGAGTGTAGAGATGAATTCTTGATAAGTTACCCTCTCCATTCCTT
1 TCCTAAACACTTCCGAGAGTGTAGAGACAAATTCTTGATAAGTTACCCTCTCCATTCCTT
* * *
2464 TCCTAAACACTTCCGAGGGTGTAGGGACAAATTCTTGATAGGTTACCCTCTCCATTCCTT
1 TCCTAAACACTTCCGAGAGTGTAGAGACAAATTCTTGATAAGTTACCCTCTCCATTCCTT
2524 TC
1 TC
2526 TTTGAATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (60 bp):
TCCTAAACACTTCCGAGAGTGTAGAGACAAATTCTTGATAAGTTACCCTCTCCATTCCTT
Found at i:2677 original size:20 final size:20
Alignment explanation
Indices: 2652--2694 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
2642 TGTGAGGATT
2652 TTTATT-TTATATT-TTATTTA
1 TTTATTATT-TATTATTA-TTA
2672 TTTATTATTTATTATTATTA
1 TTTATTATTTATTATTATTA
2692 TTT
1 TTT
2695 TATGAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTATTTATTATTATTA
Done.