Quantitative multiplexed identification of nucleic acid targets

A system for detecting in a sample at least one of a plurality of target nucleic acid molecules, the system comprising:

• a sample comprising at least one of said plurality of target nucleic acid molecules, wherein each of said plurality of target nucleic acid molecules has a first amplification region that is conserved among said plurality of target nucleic acid molecules and a second amplification region that is not conserved among said plurality of target nucleic acid molecules, wherein for each one of the plurality of target nucleic acid molecules, the first amplification region and the second amplification region are in different locations of the nucleic acid molecule;
• a first primer pair, said first primer pair capable of amplifying the first amplification region of each of said plurality of target nucleic acid molecules to produce a first amplification product;
• a real-time nucleic acid amplification instrument, wherein said instrument is capable of producing said first amplification product using said first primer pair and is further capable of detecting said first amplification product in real time;
• a second primer pair, said second primer pair mutually exclusive from the first primer pair and capable of, simultaneously with the production of the first amplification product, amplifying the second amplification region of each of said plurality of target nucleic acid molecules to produce a second amplification product,
• wherein the first amplification region and the second amplification region are in different locations of the nucleic acid molecule;
• wherein the first and second amplification products are separate products;
• and
• a detection device for detecting said second amplification product.