Fig. 3

Bernoulli, Hit Integration, and Heaviside models. The Bernoulli (for \(p = 0.7\)), the \(\int _{0.5}^{1.0}\) Hit Integration, and the \(\sum _{\frac{1}{2}}^{1}\) Heaviside probability mass functions of the number of matches, on alignments of length \(\ell =64\). Highlighted dots indicate the weights given for each alignment class with a given number of matches m out of \(\ell\) alignment symbols, under each of the three models. Note that, since the sum of the weights is always 1 for any model, and since the class of alignments with exactly \(m=32\) matches out of \(\ell =64\) is fully included in \(\sum _{\frac{1}{2}}^{1}\) Heaviside model but only half-included in \(\int _{0.5}^{1.0}\) Hit Integration model, there is a thin difference between the two resulting lines