Alignment of genomes of chloroplasts Arabidopsis thaliana and Oenothera elata. (A) ABA graph. We use BLASTZ (Schwartz et al. 2003b) with parameter “B = 1C = 2” to generate pairwise local alignments. Gray path corresponds to the direct strand of Arabidopsis DNA. The number in bold font close to an edge corresponds to the block number in B, the blockset of Blanchette et al. (2004) (Reproduced from Figure 2A in Blanchette et al. [2004]). (B, top) A dot plot of the Arabidopsis genome (horizontal axis) and Oenothera genome (vertical axis). (middle, bottom) Nine “alignment blocks”; each block contains sequence segments labeled by the genome of origin (a) = Arabidopsis, (p) = Oenothera and the coordinates of the segment in the genome.
