pilercr - software for finding CRISPR repeats
pilercr v1.06 http://www.drive5.com/piler
Written by Robert C. Edgar This software is donated to the public
domain. Please visit web site for requested citation.
- -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.