Visual representation of M-GCAT's multiple alignment of six Neisseria genomes. The horizontal lines correspond to a linear representation of each genome sequence. The vertical polygons represent the 79 M-GCAT clusters of average length 28,153 nucleotides. Evident from the visual representation of the alignment is that there are many rearrangements throughout the genome comparison. Inverted vertical polygons depict an inversion between two of the genome sequences. The small rectangles overlapping the horizontal lines correspond to the standardized MUSCLE alignment score for each respective M-GCAT cluster; darker intensities indicate better scores. In total, 82.5% of the original genome sequences are covered by the multiple alignment, and 17.5% was left unaligned. kb, kilobases.