Dotplot graphic and detailed alignment graphic. The dotplot (top) visualizes the content of the alignment scoring matrix used to calculate the global alignment with free endgaps where the reference loci (p) and target loci (q) are arranged in rows and columns, respectively. Brightness of green color indicates the relative score value (rscore) of sequence similarity for a particular locus match. The dotted squares correspond to the optimal alignment path, which is shown in the alignment drawing (black box). Swapped orientation of a single target locus (w.r.t. a matching reference locus and the cluster orientation) is indicated by shaded boxes and opposite arrow orientation in the dotplot and alignment drawing, respectively. (Note that in this example the alignment path contains only aligned loci which share the same orientation.) The focal reference gene is highlighted by a light frame and orange color in the dotplot and alignment drawing, respectively.