A processor-implemented method is provided for determining first and second indices of cell instances of a configuration memory cell of a tile module of a programmable logic device (PLD) design. A netlist is input that describes the PLD design and includes the cell instances of the configuration memory cell. An identification of the tile module is input. Characterization data is input for each configuration memory cell specifying address and data input pins. Characterization data is input for each configuration control module specifying a first ordered set of address output pins and a second ordered set of data output pins. For each of the cell instances, the first index of an address output pin in the first ordered set and the second index of a data output pin in the second ordered set are determined and a specification is output of the cell instance and the first and second indices.