Multiple sequence alignments play a central role in Bioinformatics. Most alignment representations are designed to facilitate knowledge extraction by human experts. Additionally statistical models like Profile Hidden Markov Models are used as representations. They offer the advantage to provide sound, probabilistic scores. The basic idea we present in this paper is to use the structure of a Profile Hidden Markov Model for propositionalisation. This way we get a simple, extendable representation of multiple sequence alignments which facilitates further analysis by Machine Learning algorighms.