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Beacon Designer™

Exon Junction Primer Design

Beacon Designer™ can design primers that span across exon-exon and exon-intron junctions. The exons and introns are identified by interpreting GenBank header annotations when sequences are fetched from NCBI. Alternatively, they can be specified from within the program using the "Locate Exon" function. When the exon junction primer design option is chosen, Beacon Designer locates one of the primers from the pair of primers, at the junction. The other primer from the pair is located in the gene or region of interest depending on the amplicon size and other design parameters selected. This function is especially useful for selectively amplifying cDNA from gDNA.

Beacon Designer™ software identifies exons and introns on sequences fetched from NCBI and designs primers across exon-exon and exon-intron junctions.

Exon Junction Primer Design functionality is also available in our product AlleleID.

Automate Your Real Time PCR Primer and Probe Design

Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

Specific and Efficient Design: How Beacon Designer™ Makes it Possible?

You can BLAST search sequences and search for template structures from within the program. The results of both these searches are used while designing primers and probes. The regions that exhibit significant cross homologies and template structures are avoided automatically during the design.


  • SYBR® Green Primer Design
  • TaqMan® Probe Design
  • Multiplex Real Time PCR Assay Design
  • HRMA Primer Design
  • MethyLight TaqMan® Design
  • Molecular Beacon Design
  • NASBA® Assay Design
  • FRET Probe Design
  • Scorpions® Design
  • Avoiding Cross Homology- For Specific Oligo Design
  • Avoid Template Structures- Increase Primer Efficiency
  • Oligo Rating


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