Design Primer by Variation ID

Parameter Selection

Optimal primer size:
Max primer size:
Min primer size:
Optimal primer TM:
Max primer TM:
Min primer TM:
Optimal GC percent:
Max GC percent:
Min GC percent:
Max #N's accepted:
Max Poly-X:
Max Internal Poly-X:
Max Self Complementarity:
Max 3' Self Complementarity:
Max Pair Complementarity:
Max 3' Pair Complementarity:
Product Size Ranges:

Information

This page provides a variant-centered PCR primer design module for rice. Given a SNP, INDEL, or STR identifier, the module enables users to design PCR primers flanking the target variant for experimental validation and molecular marker development. Primer design is performed using Primer3 as the backend engine.

Customizable Flanking Region: Users can specify upstream and downstream flanking lengths around the target variant, allowing flexible control over the amplified genomic region and PCR product size.

Primer Parameter Customization: Primer design parameters can be adjusted by users, including primer length, melting temperature, GC content, and product size range. This enables adaptation of primer design to different experimental conditions and platforms.

Variant-aware Primer Placement: To ensure specificity and robust amplification, the primer design process accounts for nearby polymorphic sites and avoids placing primers across other variants within the target region.

Primer and Target Visualization: Designed primers are displayed together with the target sequence and annotated genomic context, allowing users to visually inspect primer positions, target variants, and excluded regions along the amplified sequence.