Figure 3.

Location of the counting regions used for oligonucleotide scoring relative to exonic flanks. All short exons that were not able to accommodate the regions are disregarded. (A) The region arrangement for the counting strategies shown in Figures 2 (A) and (B), where the Skip value is set to 0 nt for the first comparative measurement and 29 nt for the second. The second comparative measurement is necessary to predict active intronic elements that have maximum enhancing/silencing potential at certain optimal distance from the exonic boundary, such as polyG signals [26]. The second measurement also trades the smaller number of longer exons considered for the greater chance of detecting element density discrepancy between the middle of the exons and the flanks. (B) The region arrangement corresponding to differential test strategy shown in Figure 2 (C). (C) The tiling strategy within a region increases the variety of elements sampled in a counting round. Tree different colors used to show which oligo within a region gets sampled in a three consecutive statistical tests (red in the first test, green in the second test, blue in the third test). This strategy reduces chances for multiple sampling of the same oligo conserved at a certain position in closely related organisms.