Fig. 4. Dot plot showing the correspondence of unique 101-nucleotide oligomers from the donkey scaffolds to their location on the horse genome, using exact matches.

Because the orientation of the donkey scaffolds is unknown a priori, those were oriented using the strand that minimized the number and the size of inversions with respect to the horse chromosomes. The large inversions on the donkey scaffolds aligning to ECA7, ECA28, and ECA31 are enlarged for clarity. In the enlarged alignment to ECA7, donkey scaffold ScCGjx6_197 is not reverse-complemented consistently with the figures found in the Supplementary Materials.