To do this, you will need to input the original frame rate for the YUV file into the fidelity analysis configuration window in order for the tool to line up the correct frames of raw (YUV) and encoded (MPEG) video. It's important to note however that depending on how good of a job the telecine (or whatever changed the frame rate of the resultant MPEG) did, you may get some very interesting fidelity numbers, most likely bad scores. For example, if a frame gets inserted between two others that is a blending of the frames on either side (a common practice when increasing frame rates) that frame would receive a terrible fidelity score when compared to either of the source frames as it would only be 50% of one or the other. These are the kinds of things to watch out for when doing a fidelity analysis with differing frame rates.