trf1
Locate and display tandem repeats in dna sequences
Usage
trf {(File | Match | Mismatch | Delta | PM | PI | Minscore | MaxPeriod)
[options]}
Options
Where: (all weights, penalties, and scores are positive)
File
|
sequences input file |
|---|---|
Match
|
matching weight |
Mismatch
|
mismatching penalty |
Delta
|
indel penalty |
PM
|
match probability (whole number) |
PI
|
indel probability (whole number) |
Minscore
|
minimum alignment score to report |
MaxPeriod
|
maximum period size to report |
[options] = one or more of the following:
-
-m -
masked sequence file
-
-f -
flanking sequence
-
-d -
data file
-
-h -
suppress html output
-
-r -
no redundancy elimination
-
-l <n> -
maximum TR length expected (in millions) (eg,
-l3 or-l=3 for 3 million) Human genome HG38 would need-l6
-
-ngs -
more compact .dat output on multisequence files, returns 0 on success. Output is printed to the screen, not a file. You may pipe input in with this option using - for file name. Short 50 flanks are appended to .dat output.
Note
Note the sequence file should be in FASTA format:
>Name of sequence aggaaacctgccatggcctcctggtgagctgtcctcatccactgctcgctgcctctccag atactctgacccatggatcccctgggtgcagccaagccacaatggccatggcgccgctgt actcccacccgccccaccctcctgatcctgctatggacatggcctttccacatccctgtg
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).