Exons located on the Drosophila melanogaster X chromosome sharing similar length, same splice sites and reading frames, and sequence similarity. The pie chart shows the total number of exons of the Drosohpila melanogaster X chromosome, which share the features used by the new search algorithm. The blue and red slices represent the number of exons found by the new algorithm compared to existing annotations and to the ab initio prediction by AUGUSTUS, shown in the middle. The blue part illustrates the exons already annotated by Flybase, in contrast to the exons in clusters additionally predicted by WebScipio in red. The pie is divided in slices for initial, internal, and 3'-terminal exons. In addition to the number of exons, the chart indicates the number of clusters and genes, in which these exons were found. The orange numbers in the middle part of the pie indicate how many of the respective exons are found and reconstructed with correct exon borders by the ab initio prediction with AUGUSTUS, while the yellow numbers reveal the number of exons to which exons predicted by AUGUSTUS at least overlap. The green slices indicate constitutive exons, which share the features of mutually exclusive exons. These are the same exons, clusters, and genes as listed in Table 2 and Additional file 2. At the bottom, the figure illustrates the different types of alternatively spliced exons (multiple promoters, multiple poly(A) sites, mutually exclusive exons) in comparison with the cassette exon type.