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Real Time PCR Primer Design

AlleleID® designs real time PCR primers that are optimized for the following chemistries viz. TaqMan®, TaqMan®MGB, molecular beacons and FRET. These real time PCR primers are specific, efficient and compatible with the probe that they work with:

  • Primer Specificity: Primers are designed by avoiding significant cross homologies identified by automatically interpreting BLAST search results.

  • Primer Efficiency: Primer efficiency is enhanced by automatically avoiding template structures identified by folding the template.

  • Multiplex PCR Primer Design: Design support for multiplex assays is included. Up to four sequences in the TaqMan® design mode and five sequences in the molecular beacon design mode can be multiplexed.

  • Use Pre-designed Primers: Include a well proven primer set for a template and design a compatible probe.

AlleleID® can also be used to design SYBR® Green real time PCR primers. There is a separate SYBR® Green real time primer design mode in AlleleID®.

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