Fig. 2

Alignment of assembled N67C contigs to the 17X chromosomes. The alignments were generated using progressiveMauve which uses a positional homology approach to compare the 17X genome and the N67C assemblies scaffolded. Each color corresponds to a locally collinear block (LCB) that is conserved across the two genomes. Inside each LCB, the jagged dark lines represent the similarity profile. The height of the similarity profile at a given point corresponds to the average level of conservation in that region of the genome sequence. The profile's height was calculated using an entropy model that measured deviation from randomness. The higher the profile at a given point, the more that region of the chromosome deviates from the similarity expected by random chance. Overall, the height of the similarity profile was calculated to be inversely proportional to the average alignment column entropy over a region of the alignment. Therefore, a sudden drop in the profile (a "valley") indicates a region where the similarity score between the two sequences is low. For each region, the shaded & jagged areas show the range of similarity values. The vertical red lines indicate chromosome boundaries. The regions outside the LCBs (white regions) lack detectable homology among the pair of genomes compared. Areas within the blocks that are entirely white do not align with the other