Rationale for the alignment analyses. The five horizontal blue lines represent the backbone DNA, and the triangles represent the VSs interrupting the backbone. All the VSs present at a given position of the alignment constitute a locus. (a) The five categories of VS positions relative to genes. Red arrows below the backbone blue lines represent genes. IntraG, intragenic; interG, intergenic; G, gene; L, length. (b) Loci history. VSs are colored according to DNA content. Identical color indicates identical content. Detection of insertions, deletions, ancient insertion or deletion event (ins or del), dimorph, homeologous and polymorph loci are as detailed in the text.