A wafer is transported on a blade of a robot along a path through a port into a module of semiconductor manufacturing equipment. The port has a transverse axis intersecting the path. Dynamic alignment uses two through-beam sensors positioned along the transverse axis to determine the position of the center of the wafer with respect to the center of the blade as the wafer is transported. Positioning of the sensors according to latency characteristics of the sensors assures that the moving wafer will break or make a beam of a first of the sensors and that the first sensor will generate a first transition signal before the moving wafer will break or make a beam of a second of the sensors and before the second sensor generates a second transition signal. The dynamic alignment may be performed with respect to wafers having different sizes.