Multiplex Primer Design With Varied Sizes using MP-Ref

July 21, 2025

This is an example for desinging primers with different amplicon sizes for gel electrophoresis (demo link).

1. Select the target database;
2. Enter the targets in BED format;
3. Choose “Validation method” = “[Multiplex] Size discrimination, e.g., gel electrophoresis”;.
4. And set the “Product Size Min Difference” = 20, this parameter requies the size difference of each amplicons should >= 20 bp.
5. As expected, the three amplicons have enough size differences which we can discriminate them by gel electrophoresis.