Example cases of mutually exclusive spliced exons, multiple promoters and multiple poly(A) sites. The figure illustrates three examples of genes containing mutually exclusive spliced exons, one example containing multiple promoters, and one containing multiple poly(A) sites. Dark grey bars and light grey bars mark exons and introns, respectively. The small blue bar represents an "intron?" that does not have canonical splice sites because an exon is missing in the assembly. Coloured big bars represent mutually exclusive exons found by the new algorithm. The darkest coloured bar is the exon that was included in the query sequence, while the lighter coloured bars represent identified mutually exclusive exons. The higher the similarity between the candidate and the query exon the darker will be the colour of the candidate (100% identity would result in the same colour). Yellow boxes with numbers indicate the reading frame of the corresponding exon.