An example of the output and results of the analytical method. (A) Amino acid alignments are shown for three exemplary target sequences used in the analysis (the first sequence in each alignment is the target) used in the analysis. Each destination sequence is shown for the fragment (for recombinant sequences) or whole sequences (for non-recombinant results, in these examples) that showed the homology match. Each color represents a different amino acid. (B) Mosaic ancestry of the 3D7 DBLα domains. Schematic representations of domains from the 3D7 genome showing the source of the nearest-neighbor of each homology block: 3D7 (red, within genome match, recent homology), HB3 (green, within species match, older homology) and P. reichenowi (blue, across species match, ancient homology). Homology regions are separated by black vertical lines, and adjacent blocks of the same color represent blocks originating from different genes of the same genome. Genes are placed in genomic context showing relative locations to each other and to the telomeres of each chromosome (chromosomes drawn roughly to scale). Possible pseudogenes are marked with *. Only robust, high-scoring alignments are shown. Alignments for 3D7 PF08_0140 and 3D7 PFL0020w are not shown due to poor scores.