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This will depend on the type of machine you are using. The most commonly used 5' reporter dye for Real-Time PCR is 6-FAM. This dye works in most RT-PCR machines. As to the quencher, FAM works equally well with the TAMRA dye (for FRET) and the Blackhole Quencher-1 or Iowa Black FQ.
The ABI Real-time PCR machines have filters for FAM, VIC/JOE, NED/TAMRA and ROX. This allows you to use a variety of combinations for multiplexing. These include JOE NHS, HEX, Cy3, TAMRA NHS and Texas Red. Information on the absorption and emission spectra of all dyes offered at IDT can be found at the following link by clicking on the details button of the modification you are interested in. cuturl('http://www.idtdna.com/Catalog/Modifications/Modifications.aspx?catid=3')
Additional information about multiplexing using the ABI machines can be found at the Applied Biosystems Website cuturl('http://home.appliedbiosystems.com.')
