Designs a two-strand toehold exchange probe (Complement C + Protector P) for a target you supply with the site marked as [A/G] (an SNP), [/ATG] (an insertion) or [ATG/] (a deletion), or as [A] to simply detect a fixed site with no polymorphism; IUPAC codes such as [R] also work. The Protector length and toehold are tuned so the displacement reaction is near-thermoneutral (ΔG°rxn ≈ 0) for the on-target allele, which maximises discrimination of SNPs and short indels; for a plain detection probe, set a negative target ΔG°rxn for maximum signal.
Method: Zhang, Chen & Yin (Nat Chem 2012); kinetics scale with toehold ΔG per Zhang & Winfree (JACS 2009). First-pass build: equilibrium thermodynamics only (not a kinetic simulation); mismatch penalties are approximate — see the Warnings tab.
Site marked [A] (detect a fixed site), [A/G] (SNP), [/ATG] or [ATG/] (indel). Results update as you type — open the Probe design tab to see them.
Export: click inside a result area → Ctrl+A → Ctrl+C.