Pairwise comparison of the human and mouse genome with Blockfinder and Syntenator. Dark gray bars represent the proportion of man (HSA) and mouse (MMU) genes, which could be aligned. Light gray bars represent the proportion of human and mouse genes, which fall into regions that are covered by alignments. Both number are the same for Syntenator as it considers all genes of a genome simultaneously. The "EnsEMBL Compara" bars are taken from the EnsEMBL synteny blocks. The three other runs were conducted with BlockFinder and differing sets of homology relations (see text). The number to the right of each bar is the proportion relative to the total gene set in percentage.