Reconstructing short exons at low homology intron borders. The scheme shows two examples for the reconstruction of short exons in regions where the intron borders of the neighbouring exons show some homology to the unmatched query sequence. The value for the --max_move_exon parameter has been set to 3 (case A) and 6 (case B), respectively. The colour coding of the scheme is the same as in Figure 3. For further information see Additional file 2.