Extended sequence models. Graphical representation of the three linear weights models we studied that factor sequence information beyond the ACS. The paired linear model (A) is using an auxiliary motif in addition to the ACS PWM: the overall score is the weighted sum of the individual (disjoint) match scores. The contextual PWM model (B) consists of the weighted sum of the ACS match and the adjacent matches to the contextual PWMs. The latter are learned from the sites flanking the ACS sites in the alignment of the native ARSs. The Markov contextual model (C) combines the ACS match with the (log of the) Markov likelihood of the adjacent segments (normalized by an iid background model). The contextual Markov models are learned from the alignment of the native ARSs.