Relationship between improvement of alignment accuracy and benchmark difficulty. The relative improvement of the alignment accuracy (Y-axis) calculated as improvement of SP (Sum-of-Pair) score is plotted against the quality of alignment input to REFINER, as measured by three objective scoring functions (X-axis). a) Conservation (SCORECONS) score b) norMD score c) information content. The central line in each box shows the median value, the upper and lower boundaries of individual box show the upper and lower quartiles, and the vertical lines extend to a value 1.5 times the inter quartile range. Outlier values are shown outside the whiskers.