Dot-plot alignments of a 2.9 Mbp chromosome of A. fumigatus (x-axis) to a 2.1 Mbp scaffold of A. nidulans (y-axis). Left: nucleotide-based alignment with Nucmer. Right: amino-acid-based alignment with Promer. Aligned segments are represented as dots or lines, up to 3,000 bp long in the Nucmer alignment and up to 9,500 bp in the Promer alignment. These alignments were generated by the mummerplot script and the Unix program gnuplot.