Occurrence of extensions ( E = 1,2,...,18 nucleotides) for A5Es (parts A, C) and A3Es (B, D), with human and mouse exons in the top and bottom panels, respectively. Extensions were inferred from three different alignment algorithms (colored as blue, SIM4; red, BLAT; and green, EXALIN) of cDNAs/ESTs to genomic DNA. The distribution f(E) for A5Es was markedly biased for extensions (E) with overlapping splice sites, with a peak at E = 4 nucleotides. Exon extensions exhibited relatively smaller but persistent periodic peaks at E = 6, 9, 12, 15, and 18 nucleotides. f(E) for A3Es also displayed a bias for overlapping splice sites, with a peak at E = 3 nucleotides and smaller peaks at 4–6 nucleotides. The program SIM4 predicted significantly more extensions at E = 4 nucleotides as compared to BLAT and EXALIN predictions of the same initial set of cDNAs/ESTs, which was indicative of spurious alignments. A comparative analysis of alternative exons in M. musculus corroborated the above patterns.