KASP Primers Genotyping Assay Design Tool

KASP (Kompetitive Allele Specific PCR) / PACE (PCR Allele Competitive Extension) / ASQ (Allele-Specific Quantitative PCR) genotyping assay design for multiallelic discrimination of single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) at specific loci. The application provides professional facilities for genotyping assay design for SNP/InDel-specific KASP assay-targeting primers (KASP Assay Mix).

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

Human rsIDs:

Flank size (±bp):

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

Upload FASTA:

Reverse Primer Design Options

Length range (nt)

–

Tm range (°C) for standard PCR conditions

–

3′-end pattern (5′-3′)

SNP at 3′-end of Allele-specific primer (ASP)

Specificity

Non-specific priming control

Low complexity priming control

Allow overlapping primer positions

Methylation

C→T bisulfite conversion (methylation analysis)

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