The present disclosure relates to a computer-implemented method for assigning pins in an electronic design. The method may include generating a pin list associated with the electronic design, the pin list having a one or more pins that are directly and indirectly connected with at least one of a master partition and a clone partition. The method may further include sorting one or more pins within the pin list based upon, at least in part, a number of local connections to generate a sorted pin list and selecting a first pin having a highest number of local connections of the sorted pin list as a reference pin. The method may also include selecting a partition of the reference pin, as a reference partition and identifying one or more alignment zones for every connected pair of pins in the sorted pin list. The method may further include transforming all alignment zones to the reference partition using a depth-first-search.