KASP™ (Kompetitive Allele Specific PCR) / ASQ genotyping assay design for multiallelic discrimination oof 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).
Format variants as [A/G], [IUPAC], or [allele1/allele2/allele3/allele4]. Supports haplotypes, MNVs, and InDels.
Input format: Sequence(s) can be pasted or uploaded as a file in FASTA format or retrieved flanked sequence SNP sequences from NCBI’s database. One or multiple SNP/variant rsIDs (comma or space separated: rs56116432, rs123, rs999) were used to retrieve the surrounding sequence (±flank bases) for the Homo sapiens genome only.
Variant formats:
- 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.