This mode designs primer pairs in multiple windows around your selected region of interest (typically upstream / internal / downstream) to support structural variant validation. Provide chromosome, start/end coordinates, and choose the variant type.
These values are submitted with your design request. PCR / qPCR presets set target padding and the usual product size range (you can still edit afterward). Advanced keys override the built-in Primer3 defaults when set; leave Tm min/max blank to derive from optimal Tm ±2 °C.
PCR: target padding 50 bp per side, product size 400–800 bp. qPCR: padding 30 bp per side, product size 80–150 bp.
Leave blank to derive from optimal Tm ±2 °C. Otherwise overrides min/max.
Finding optimal primer pairs for your variant.
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