---
name: "primers"
section: "1e"
platform: "linux"
package: "emboss"
version: "6.6.0+dfsg-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/primers"
---

# primers(1e)

Simple version of primer3 to pick PCR primers

## NAME

primers - Simple version of primer3 to pick PCR primers

## SYNOPSIS

**primers** **-sequence** *seqall* \[**-targetregion** *range*\] \[**-minsize** *integer*\] \[**-maxsize** *integer*\] \[**-maxdifftm** *float*\] \[**-explainflag** *boolean*\] \[**-numreturn** *integer*\] **-outfile** *outfile*

**primers** **-help**

## DESCRIPTION

**primers** is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Nucleic:Primers" command group(s).

## OPTIONS

### Input section

- **-sequence** *seqall*

  The sequence from which to choose primers. The sequence must be presented 5' -\> 3'

### Additional section

- **-targetregion** *range*

  If one or more Targets is specified then a legal primer pair must flank at least one of them. A Target might be a simple sequence repeat site (for example a CA repeat) or a single-base-pair polymorphism. The value should be a space-separated list of \<start\>,\<end\> pairs where \<start\> is the index of the first base of a Target, and \<end\> is the last E.g. 50,51 requires primers to surround the 2 bases at positions 50 and 51.

- **-minsize** *integer*

  Minimum acceptable length of a primer. Must be greater than 0 and less than or equal to MAX-SIZE. Default value: 18

- **-maxsize** *integer*

  Maximum acceptable length (in bases) of a primer. Currently this parameter cannot be larger than 35. This limit is governed by the maximum oligo size for which Primer3's melting-temperature is valid. Default value: 27

- **-maxdifftm** *float*

  Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers. Default value: 100.0

### Output section

- **-explainflag** *boolean*

  If this flag is non-0, produce LEFT-EXPLAIN and RIGHT-EXPLAIN, output, which are intended to provide information on the number of primer pairs that Primer3 examined, and statistics on the number discarded for various reasons. Default value: N

- **-numreturn** *integer*

  The maximum number of primer pairs to return. Primer pairs returned are sorted by their 'quality', in other words by the value of the objective function (where a lower number indicates a better primer pair). Caution: setting this parameter to a large value will increase running time. Default value: 5

- **-outfile** *outfile*

  ## BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group\_id=93650&atid=605031).

## SEE ALSO

primers is fully documented via the **tfm**(1) system.

## AUTHOR

**Debian Med Packaging Team** \<debian-med-packaging@lists.alioth.debian.org\>

Wrote the script used to autogenerate this manual page.

## COPYRIGHT

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.