Column reliability plot for 1csy_ref1 from BAliBASE, Reference 1. The red line and solid regions indicate the predicted and actual proportion of correct pairwise matches at each alignment position, respectively. All column reliability values have been multiplied by 100. Below, the actual ProbCons alignment is shown with core block residues highlighted in green. Note that only pairwise matches in core block regions of the BAliBASE alignment are considered correct when computing the “actual” proportion of correct pairwise matches; however, some residues outside of the core block regions may also be alignable. Thus, regions in which predicted homology exceeds actual homology do not necessarily indicate overprediction of homology by the aligner.
