Abstract: Provided herein are methods and systems for detecting the presence or absence of multiple target nucleic acids in partitions of a digital amplification assay. In one embodiment of the method, different probes labeled with the same signal-generating label are distinguishable from each other as a result of having different melting temperatures in the presence of their cognate target nucleic acids. Following amplification of the target nucleic acids in a digital assay, signals are measured at three or more different temperatures and at least two relational values between signals measured at the three or more different temperatures are calculated and plotted against each other to classify partition subsets according to their target nucleic acid occupancy.