Illustration of simple de novo annotation. Shown is a comparison of two aligned protein orthologs, each of which is 27 amino acids in length. Filled circles between the sequences indicate sites at which the amino acids are distinct The sequence has been segmented into red (more slowly evolving) and green (more rapidly evolving) regions to illustrate the biological motivation. The figure above the alignment shows, for each of positions 3 through 25, the fraction of mismatched amino acids among positions j - 2 through j + 2 plotted as a function of j (highlighted for j = 3 in gray). The region from positions 8 to 12 shows a deficit of changes, suggesting the possible presence of a conserved domain.