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PRIMERS(1e) EMBOSS Manual for Debian PRIMERS(1e)


primers - Simple version of primer3 to pick PCR primers


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

primers -help


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).


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 can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


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


Debian Med Packaging Team <>

Wrote the script used to autogenerate this manual page.


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.

05/11/2012 EMBOSS 6.4.0