The above seems like a very unnatural thing to do, so let me elaborate a little more on my research question. I want to develop a PCR reaction that serves both to detect a pathogen and also gives information about the genotype. My idea was to do this in one amplicon, which allows different grades of specificity. My primers are relatively conserved sequences that flank a variable region that contains repeat sequences. If it amplifies at all (which one would detect with SYBR), I know the genus of pathogen is present. The probes would be against unique sequences that identify a few major species (but cannot be exhaustive).

I realize that I can also use a general probe to detect the presence of a product (in fact, that is what I'm actually doing), but it's more prone to false negatives in case of mutations and I don't get information about amplicon length as one gets with SYBR green melt curves (see repeat sequences). Obviously quantification of expression (which is hard to compare between SYBR and Taqman) is explicitly not an issue.

There are many reasons why the above is impractical, for one the PCR machine software would probably not play ball and the broad emission spectrum of SYBR emission might make a few channels unusable, but is it possible in theory?