Multiplex PCR Primer Design for Repeat Region (SMN1 whole gene) with MP-Ref

Multiplex PCR Primer Design for Repeat Region (SMN1 whole gene) with MP-Ref

July 21, 2025
Application, MP-Ref
Primer Design, Multiplex PCR, MP-Ref

Primer Design for SMN1 Whole Region #

The whole genome sequence of SMN1 has a near identical repeat sequences is from SMN2. Primers for SMN1 also can amplify sequences from SMN2 and can’t be avoidable. So for NGS validation, mutations from amplicons sequencing may need to further validation, like Sanger sequencing, which design primers with amplicon size large engouth to skip the repeat region.

https://m4.igenetech.com/muld/demo/e7cd1164-3441-4a50-8c76-1862ef09f6aa

  • Input: chr5 70924941 70953012;
  • Genome: hg38;
  • Set “Min=0” for “Minimum Nucleotide Differences”, otherwise, MP-Ref will run 20+ hours to find very specific primers and will fail eventually.
  • Other options: default

Input

Output