KASP™ (Kompetitive Allele Specific PCR) / ASQ 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).
Input format: Sequences can be pasted or uploaded as a FASTA-formatted file, or flanking SNP sequences can be retrieved from the NCBI/Ensembl database. One or more SNP/variant rsIDs (separated by commas or spaces: rs56116432, rs123, rs999) can be used to retrieve the surrounding sequence (± flanking bases) for the target genome.
Variant formats: as [A/G], [IUPAC], or [allele1/allele2/allele3/allele4].
- SNP:
[A/G]or[R](IUPAC code) - InDel:
[AG/]for insertion/deletion - MNV:
[GATATACTTGAG/CAGTCC] - Haplotype: Multiple SNPs within one bracket pair
Standard tails: FAM: 5′-GAAGGTGACCAAGTTCATGCT-3′ | HEX: 5′-GAAGGTCGGAGTCAACGGATT-3′
Quick Help for KASP Assay Design
- Define the variant as [R] (IUPAC) or [allele1/allele2]; haplotypes can be inside one bracket pair.
- Optionally retrieve flanked variants via Ensembl (species + rsIDs) and set an appropriate flank size.
- If allele-specific tails are custom, paste them in the 'tails list' tab before running.