MFEprimer-4.4.0: PCR Primer Design and Quality Control Tools

* Primer sequences (<= 1000?) (FASTA format or just plain sequences one per line, example, clear)

Potential hairpin settings

Min loop size

Min

Max loop size

Max

Min double helix size

Min

Allowed max gaps for a hairpin

Max

Score (base pairs)

Min

Score cutoff value to filter hairpins

ΔG

Max

kcal/mol

ΔG cutoff value to filter hairpins

Thermodynamic settings

Concentration of monovalent cations (usually KCl)

Concentration of divalent cations (usually MgCl₂)

Concentration of dNTPs

Annealing oligo concentration

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Hairpin analysis