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The design of efficient locomotion controllers for arbitrary structures of reconfigurable modular robots is challenging because the morphology of the structure can change dynamically during the completion of a task. In this paper, we propose a new method to automatically generate reduced Central Pattern Generator (CPG) networks for locomotion control based on the detection of bio-inspired sub-structures, like body and limbs, and articulation joints inside the robotic structure. We demonstrate how that information, coupled with the potential symmetries in the structure, can be used to speed up the optimization of the gaits and investigate its impact on the solution quality (i.e. the velocity of the robotic structure and the potential internal collisions between robotic modules). We tested our approach on three simulated structures and observed that the reduced network topologies in the first iterations of the optimization process performed significantly better than the fully open ones.