ORF-by-ORF alignments of PA14 and PAO1. Each predicted ORF in PA14 was compared using BLAST with all annotated PAO1 ORFs, and the best match was indicated as a single data point with the chromosomal locations of the match in each genome. Reciprocal BLAST searches were also performed (using individual PAO1 ORFs against the complete set of PA14 ORFs). Matches in the forward direction are indicated by red diamonds, and matches in the reverse orientation are indicated by blue diamonds. Genes that fall outside of the diagonals (non-colinear genes) are a combination of translocations and gene pairs in which a true ortholog is missing in one strain but a similar gene exists elsewhere in its genome and the two genes have been selected as reciprocal best BLAST matches. Genes in one genome that fail to have a BLAST match counterpart in the other genome are represented on the x-axis for PA14-specific genes (green diamonds) and on the y-axis for PAO1-specific genes (pink diamonds). The GC contents for each genome are represented next to the two axes using a light-blue graph; the positions that correspond to GC contents of 30%, 50%, and 70% are indicated. BLAST, basic local alignment search tool; ORF, open reading frame.