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Latest news (9 Feb 10): a multi-threaded motif finder (nz.ac.massey.cs.gql4jung.jmpl.MultiThreadedGQLImpl) is now ready to use. All test cases pass, the engine can be instantiated passing the number of threads as parameter. Setting this number to the number of cores / processors works best. Here are some results from searching for CD instances in xalan on a Xeon E5440 8-core box running RHL: 1 thread - 154s, 2 threads - 82s, 4 threads - 48s, 8 threads - 37s. However, on a MacBook Pro the same to