---
name: "pilercr"
section: "1"
platform: "linux"
package: "pilercr"
version: "1.06+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pilercr"
---

# pilercr(1)

software for finding CRISPR repeats

## 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).