Design PCR primers for a given DNA template with configurable length, Tm range, and GC content — primers are ranked by a weighted score accounting for Tm, GC%, self-complementarity, and hairpin formation. Use this tool when setting up colony PCR, diagnostic PCR, or subcloning amplifications where good primer design is critical for specificity. The output includes paired forward and reverse primers with Tm differences and amplicon sizes, calculated via the nearest-neighbor thermodynamic model for accurate melting temperature predictions.

Features

• Primer Ranking: Weighted scoring based on Tm, GC%, self-complementarity, and hairpin formation
• Configurable Parameters: Adjustable primer length, Tm range, and GC% range
• Tm Calculation: Nearest-neighbor (SantaLucia 1998) and Wallace rule methods
• Dimer & Hairpin Check: Detects self-complementarity and hairpin formation
• Amplicon Sizing: Automatic pair ranking with Tm difference and amplicon size
• CSV Export: Download top primer pairs as CSV