PCR primer design tool

End-to-end primer and probe design for standard/inverse PCR, multiplex, quantitative fluorescence assays (TaqMan/MGB), bisulfite PCR, and Recombinase Polymerase Amplification (RPA).

Supports SNP and InDel genotyping with validated primer sets for qPCR and rapid isothermal RPA.

Retrieve flanking sequence from Ensembl by rsID — validates species, fetches forward-strand context with allele bracket

Species:

rsIDs:

Enter Ensembl species id (lowercase, underscores). Custom species are stored in this browser.

Flank size (±bp):

Retrieve sequence from NCBI by accession — chromosomes (NC_), mRNA (NM_), RefSeq contigs

NCBI Accession:

Upload local FASTA file — plain FASTA, multi-FASTA, or sequences

Upload FASTA:

Primer Design Options

Length range (nt)

–

Tm range (°C)

–

PCR product size (bp)

–

3′-end pattern (5′-3′)

Forward tail (5′-3′)

Reverse tail (5′-3′)

Non-specific priming control

Overlapping primers

Multiplex PCR

Inverse PCR (circular)

MGB-probe assay

TaqMan-probe assay

C→T bisulfite conversion

Recombinase Polymerase Amplification (RPA)

Need details? Sequence markup, parameters, output columns and the suggested workflow are documented in Help: PCR tool · Help: Troubleshooting
Exporting results: click inside the result area → Ctrl+A → Ctrl+C → paste into Excel.