NAME

       trf - locate and display tandem repeats in DNA sequences

SYNOPSIS

       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, -l 3 or -l=3 for 3 million) Human
              genome HG38 would need -l 6

       -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.

SEE ALSO

       See     more     information     on     the     TRF     Unix      Help      web      page:
       https://tandem.bu.edu/trf/trf.unix.help.html

NOTE

       Note the sequence file should be in FASTA format:

       >Name     of     sequence     aggaaacctgccatggcctcctggtgagctgtcctcatccactgctcgctgcctctccag
       atactctgacccatggatcccctgggtgcagccaagccacaatggccatggcgccgctgt
       actcccacccgccccaccctcctgatcctgctatggacatggcctttccacatccctgtg

AUTHOR

       Copyright © 1999-2020 Gary Benson

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.