We use discrete Morse theory to determine the M\"obius function of posets ordered by generalized factor order. Ordinary factor order on the Kleene closure A*A of a set A is the partial order defined by letting u if w contains u as a subsequence of consecutive letters. The M\"obius function of ordinary factor order was determined by Bj\"orner. Using Babson and Hersh's application of Robin Forman's discrete Morse theory to lexicographically ordered chains, we are able to gain new understanding of Bj\"orner's result and its proof. We generalize the notion of factor order to take into account a partial order on the alphabet A and, relying heavily on discrete Morse theory, give a formula in the case where each letter of the alphabet covers a unique letter.
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