KASP / ARMS Allele-Specific Primers
kasp_primer_designDesign KASP/ARMS allele-specific genotyping primers for a SNP: two allele-specific forward primers differing only at the 3' terminal base (one per allele), each with the standard KASP universal tail (FAM for allele A, HEX for allele B), a deliberate internal ARMS secondary mismatch near the 3' end whose strength complements that primer's own natural allele mismatch (strong↔weak), and one common downstream reverse primer sized to a chosen amplicon range. Because a forward primer reads the antisense strand, each primer's 3' base sits opposite the complement of the other allele, so the two primers get different mismatch classes and are reported separately (graded from the measured PCR yields in Kwok et al. 1990). Reuses the site's nearest-neighbor Tm engine.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| target | Yes | Nucleotide sequence (raw or FASTA; IUPAC accepted). | |
| alleleA | Yes | First allele (single base) — gets the FAM tail. | |
| alleleB | Yes | Second allele (single base) — gets the HEX tail. | |
| maxAmplicon | No | Maximum amplicon length for the common reverse primer. | |
| minAmplicon | No | Minimum amplicon length for the common reverse primer. | |
| snpPosition | Yes | 1-based position of the SNP on the forward strand. Must be 18 or greater: the allele-specific primers end on the SNP, so they need at least 17 bp of upstream template to build a core from. | |
| targetCoreTm | No | Target Tm (°C) for the allele-specific primer core (before the universal tail). | |
| addSecondaryMismatch | No | Engineer the internal ARMS destabilising mismatch near the 3' end. |