Dot plots of similarities in A. thaliana chromosomes 1 and 2 Chromosome 1 is shown to the top and left, chromosome 2 on the bottom and right. Dots represent BLASTP similarities at bit score thresholds of 500. Synteny blocks identified by DiagHunter [20,21] are shown in black (larger images are available at ). Hits of proteins to themselves have been suppressed. A large excess of local duplications is apparent in higher densities near the main diagonal. The average density at any given distance between genes can be calculated from diagonal strips through the dot plot. One such strip is highlighted in chromosome 2 × 2.