There is no inbuilt facility to compare one application with another, although if you are using different TWS subsystems as I suspect, obviously this would not be possible anyway. You will need to unload the applications and then do some post processing on the unloads to compare them. The simplest way to unload an application(s) is to use the PIF utility program (EQQYCAIN). Specify SYSIN statements similar to this -
A simple comparison of the unloads will be no good as the durations will certainly be different and possibly other values such as work station names as well. Extract the details you need that should be identical and then compare the results.