Written by Robert C. Edgar This software is donated to the public domain. Please visit web site for
requested citation.
Basicoptions:-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.
CriteriaforCRISPRdetection,defaultsinparentheses:-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.
Parametersforcreatinglocalalignments:-minhitlength <L>
Minimum alignment length (16).
-minid <F>
Minimum identity (0.94).
pilercr 1.06+dfsg August 2021 PILERCR(1)
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