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Can you recommend software packages to help design dual-labeled probes?

IDT has 2 dedicated qPCR tools for dual-labeled probe design. The PrimeTime® qPCR Assay Selection Tool is optimized for human, mouse, and rat transcripts and, as a default, selects assays that span exon junctions and avoid SNPs. This tool is updated regularly with the latest NCBI builds. If you are working with a species other than human, mouse, or rat, IDT offers the RealTime PCR tool. This tool has an expanded species list and also allows for FASTA transcript entries to design assays for any target. Both tools are freely available through the IDT SciTools® suite at www.idtdna.com/scitools).