Probability for an alignment block assuming a site occurs in the reference sequence. In the top right an alignment segment S[i,l]is shown for the species S. cerevisiae (the reference), S. paradoxus, S. mikatae, and S. bayanus. First we check which sequences are gaplessly aligned with the reference. In this case S. mikatae contains a gap and the background model is assigned to this sequence. The reference has the WM model assigned by default (indicated in red). In the left the probabilities of the sequences from S. paradoxus and S. bayanus are compared with the WM (shown as a logo). It turns out the S. paradoxus sequence scores better for the WM than for background but the S. bayanus sequence scores better to background than to the WM, because of some mismatches to the WM consensus (bases in purple). Finally, on the bottom right the phylogenetic tree is indicated with the branches that evolve according to the WM in red, and those evolving according to the background in black.