Design Primer by SNP/INDEL ID:

This tool is intended for researchers to pick PCR-primers to validate SNPs/INDELs or develop molecular markers, using Primer3 as a backend engine. Please input one SNP or INDEL ID (e.g., sf0100014574 or vf1200001047) and select upstream and downstream regions (default is 100 bp). All the parameters can be changed if necessary.


Parameter Selection:

Optimal primer size:
Max primer size:
Min primer size:
Optimal primer TM:
Max primer TM:
Min primer TM:
Optimal GC percent:
MAX GC percent:
MIN GC percent:
Max #N's accepted:
Max Poly-X:
Max Internal Poly-X:
Max Self Complementarity:
Max 3' Self Complementarity:
Max Pair Complementarity:
Max 3' Pair Complementarity:
Product Size Ranges: