Densities of homologs by genomic distance in A. thaliana chromosome 2 and genome-wide The graph on the left (3A) shows average densities in 100 kb diagonal strips through the chromosome 2 × 2 dot plot of similarities. The value at any position in the graph represents the number of homologs between 100 kb windows around a query location and a target location. The graph on the right (3B) shows similar density measurements, but within 5 kb windows and spanning up to 200 kb between genes. The x-axis measures the difference between the query and target locations. The thin line shows the density-by-distance plot for chromosome 2 × 2. The bold line shows the comparable plot for the whole genome, with scores averaged across all five A. thaliana chromosome comparisons. The red dotted line shows the best-fit exponential equation to the whole-genome curve, fitted from 5 kb to 100 kb.