Complex pattern queries play a critical role in many applications that must efficiently search databases and data streams. Current techniques support the search for multiple patterns using deterministic or non-deterministic automata. In practice however, the static pattern representation does not fully utilize available system resources, subsequently suffering from poor performance. Therefore a low overhead auto-reconfigurable automaton is needed that optimizes pattern matching performance. In this paper, we propose a dynamic system that entails the efficient and reliable evaluation of a very large number of pattern queries on a resource constrained system under changing stress-load. Our system prototype, Morpheus, pre-computes several query pattern representations, named templates, which are then morphed into a required form during run-time. Morpheus uses templates to speed up dynamic automaton reconfiguration. Results from empirical studies confirm the benefits of our approach, with three orders of magnitude improvement achieved in the overall pattern matching performance with the help of dynamic reconfiguration. This is accomplished only with a modest increase in amortized memory usage.