Figure 3.

Internal duplications within portions of Arabidopsis chromosome 1 (whole chromosome). (a) A comparison based on predicted genes. (b) A comparison based on a similarity search between all 1 kb nucleotide segments from the TIGR chromosome 1 assembly. The region in the black rectangle in (a) is shown in Figure 1. In the protein-protein comparison (a), hits with between genes with Watson-Watson or Crick-Crick ('forward diagonal') orientations are shown in red, and hits between genes with Watson-Crick or Crick-Watson ('reverse diagonal') orientations are shown in pink. The use of strand orientation in the protein-protein comparison helps to explain the greater sensitivity of this search, compared with the nucleotide comparison in (b). The dense centromeric region encompassing the main diagonal in the nucleotide-nucleotide comparison was excluded from this search.