---
name: "e-PCR"
section: "1"
platform: "linux"
package: "ncbi-epcr"
version: "2.3.12-1-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/e-PCR"
---

# e-PCR(1)

Find sequence tagged sites (STS) in DNA sequences

## NAME

e-PCR — Find sequence tagged sites (STS) in DNA sequences

## SYNOPSIS

**e-PCR \[-hV\] \[posix-options\] stsfile \[fasta ...\]** \[*compat-options\]*

## DESCRIPTION

*The program substitutes blast in the location of pairs primers on the* *genome that may yield a PCR product.*

## OPTIONS

*posix-options are:*

- **-m=***##*

  *Margin (default 50)*

- **-w=***##*

  *Wordsize  (default 7)*

- **-n=***##*

  *Max mismatches allowed (default 0)*

- **-g=***##*

  *Max indels allowed (default 0)*

- **-f=***##*

  *Use ## disontiguous words, slow if ##\>1*

- **-o=***##*

  *Set output file*

- **-t=***##*

  *Set output format:*

-

  *1 - classic, range (pos1..pos2)*

-

  *2 - classic, midpoint*

-

  *3 - tabular*

-

  *4 - tabular with alignment in comments (slow)*

- **-d=***##-##*

  *Set default size range (default 100-350)*

- **-p=***+-*

  *Turn hits postprocess on/off*

- **-v=***##*

  *Verbosity flags*

- **-a=***a\|f*

  *Use presize alignments (only if gaps\>0), slow*

-

  *a - Always or f - as Fallback*

- **-x=***+-*

  *Use 5'-end lowercase masking of primers (default -)*

- **-u=***+-*

  *Uppercase all primers (default -)*

*compat-options (duplicate posix-options) are*

- **M=***##*

  *Margin (default 50)*

- **W=***##*

  *Wordsize  (default 7)*

- **N=***##*

  *Number of mismatches allowed (default 0)*

- **G=***##*

  *Max indels allowed (default 0)*

- **F=***##*

  *Use ## discontinuous words*

- **O=***##*

  *Set output file to ##*

- **T=***##*

  *Set output format (1..3)*

- **D=***##-##*

  *Set default size range*

- **P=***+-*

  *Postprocess hits on/off*

- **V=***##*

  *Verbosity flags*

- **A=***a\|f*

  *Use presize alignments (only if gaps\>0), slow*

-

  *a - Always or f - as Fallback*

- **X=***+-*

  *Use 5'-end lowercase masking of primers (default -)*

- **U=***+-*

  *Uppercase all primers (default -)*

- **-mid**

  *Same as T=2*

*For information about further options just call* **e-PCR** without any options.

## SEE ALSO

/usr/share/doc/ncbi-epcr/README.txt

bioperl(1), re-pcr(1)

## AUTHORS

This manual page was written by Steffen Moeller \<moeller@debian.org\> and Andreas Tille \<tille@debian.org\> for the **Debian** system (but may be used by others).  Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.