NAME

       pilercr - software for finding CRISPR repeats

DESCRIPTION

       pilercr v1.06 http://www.drive5.com/piler

AUTHOR

       Written  by  Robert  C. Edgar This software is donated to the public domain.  Please visit
       web site for requested citation.

   Basic options:
       -in <filename>
              Sequence file to analyze (FASTA format).

       -out <filename>
              Report file name (plain text).

       -seq <filename>
              Save consensus sequences to this FASTA file.

       -trimseqs
              Eliminate similar seqs from -seq file.

       -noinfo
              Don't write help to report file.

       -quiet Don't write progress messages to stderr.

   Criteria for CRISPR detection, defaults in parentheses:
       -minarray <N>
              Must be at least <n> repeats in array (3).

       -mincons <F>
              Minimum conservation (0.9).  At least N repeats must have identity >=  F  with  the
              consensus  sequence.  Value is in range 0 .. 1.0.  It is recommended to use a value
              < 1.0 because using 1.0 may suppress true arrays due to boundary misidentification.

       -minrepeat <L>
              Minimum repeat length (16).

       -maxrepeat <L>
              Maximum repeat length (64).

       -minspacer <L>
              Minimum spacer length (8).

       -maxspacer <L>
              Maximum spacer length (64).

       -minrepeatratio <R>
              Minimum repeat ratio (0.9).

       -minspacerratio <R>
              Minimum spacer ratio (0.75).  'Ratios' are defined as minlength / maxlength, thus a
              value  close  to  1.0  requires lengths to be similar, 1.0 means identical lengths.
              Spacer lengths sometimes vary significantly, so the default ratio  is  smaller.  As
              with -mincons, using 1.0 is not recommended.

   Parameters for creating local alignments:
       -minhitlength <L>
              Minimum alignment length (16).

       -minid <F>
              Minimum identity (0.94).