Figure 2

Simulation statistics. Pairwise alignments were simulated for a range of divergence distances, using a modified version of the ROSE simulation platform under four different regimes: A) without constrained blocks and without insertion/deletion evolution; B) without constrained blocks and with insertion/deletion evolution; C) with constrained blocks and without insertion/deletion evolution; D) with constrained blocks and with insertion/deletion evolution. For each divergence distance, 1,000 replicates were used to calculate the mean and standard error for the following statistics: estimated overall divergence (black boxes), estimated divergence in constrained blocks of sites (grey circles), estimated divergence in unconstrained blocks of sites (brown triangles), identity (red crosses), identity in constrained blocks (yellow x's), identity in unconstrained blocks (green diamonds), fraction of ancestral sequence remaining in derived sequences (green triangle), and fraction of constraint (light blue checked boxes). Note that the divergence scale in this and following figures is discontinuous.