Primer GC Content Calculator
FREE TOOL
0 bases
0 bases
0 bases
0 primers (max 20)
Analyze GC percentage, AT/GC ratios, and perform 3' end GC clamp checks for optimal primer design and specific PCR amplification.
GC content directly affects primer melting temperature and PCR specificity. A primer with a balanced GC ratio will bind stably to the template. Extremely low GC content (<40%) leads to weak annealing and low PCR yields, while high GC content (>60%) requires high denaturation temperatures and increases secondary structure/hairpin risks.
GC Clamp: This refers to the presence of G or C bases in the last few bases of the 3' end of the primer. Having 1 to 2 G/C bases in the last 5 bases at the 3' end is standard to ensure strong and stable annealing where the extension begins. However, having more than 3 G/C in the last 5 bases can cause mispriming and non-specific bands.