Figure 3.

Sample display created by the MapView program, showing a 185 kbp slice of D. melanogaster chromosome 2L and its alignment to D. pseudoobscura. The alignment, generated by Promer, shows all regions of conserved amino acid sequence. The blue rectangle spanning the figure represents the reference (D. melanogaster), with annotated genes shown above it. Alternative splice variants of the same gene are stacked vertically. Exons are shown as boxes, with intervening introns connecting them. The 5' and 3' UTRs are colored pink and blue to indicate the gene's direction of translation. Promer matches are shown twice, once just below the reference genome, where all matches are collapsed into red boxes, and in a larger display showing the separate matches within each contig, where the contigs are colored differently to indicate contig boundaries. The vertical position of the matches indicates their percent identity, ranging from 50% at the bottom of the display to 100% just below the red rectangles.