Calculation of sensitivity and specificity of alignments. Dotted squares (A), (B), and (C) indicate homologous regions corresponding to homologous exons in an orthologous gene pair (bold square). The thin diagonals indicate the true alignments, while the bold diagonals indicate the observed alignments. Examples of true positive, false positive, and false negative are shown. In this case, region (A) is partly aligned, (B) is not aligned, and (C) is entirely aligned. The regions (b) and (e) are true positives, (a) and (d) are false negatives, and (c) and (f) are false positives.