This page provides a region-based PCR primer design module for rice. Users can specify a genomic interval and design PCR primers that amplify the selected region while targeting genetic variants located within it. Primer design is performed using Primer3 as the backend engine.

Multi-variant Targeting Within a Region: When multiple variants are present within the selected interval, the primer design process accounts for all variant positions simultaneously, allowing amplification of regions that harbor one or more polymorphic sites.

Primer Parameter Customization: sers can customize primer design parameters, including primer length, melting temperature, GC content, and PCR product size range, enabling adaptation to diverse experimental requirements.

Variant-aware Primer Design Strategy: Primer placement is guided by variant positions within the region, ensuring that designed primers effectively flank polymorphic sites and support robust genotyping and marker development.

Primer and Target Visualization: Designed primers are displayed together with annotated target regions along the genomic sequence, allowing users to visually inspect primer locations, variant targets, and the amplified region.