MP-Ref: Multiplex PCR Primer Design for Reference Genomes

Introduction Parameters help Examples

Target settings

: primers should be chosen around (not within) the regions.
NGS or Gel electrophoresis
bp
Only for size discrimination method, e.g., gel electrophoresis.

Quality control settings 1

Min
°C
The minimum binding stability between primer and its binding sites.
From
To
Product size: 0 (min) - 1000000 (max).
Min
Max
Number of non-specific amplicons.
Min
kcal/mol
Primers with dimer stability exceeding this threshold will be discarded.
Min
Primers with hairpin stability exceeding this threshold will be discarded.
Min
Minimum number of different bases between target amplicon and off-targets if allowed.
Min
bp
SNP-free region length from primer 3' end.
Min
bp
InDel-free region length from primer 3' end

Quality control settings 2 (optional)

Min
Max

Primer settings

bp
bp
bp
%
%
%
°C
°C
°C

Product settings

%
%
%
bp
bp
⚠️ 扩增子长度 >5000 bp 将导致设计时间极长，计划 2026-06-04 起限制为 5000 bp。Amplicons >5000 bp will cause extremely long design times; limit to 5000 bp planned from 2026-06-04.

Thermodynamic settings

mM
mM
mM
nM

🧬 Powered by
iGeneTech Bioscience

Target Gene Enrichment Expert

Custom NGS Panels Library Prep Kits
Explore Products →
Contact
Request more input?

For bug reports or suggestions, please email us.