Positively weighted scaffolds in the Eponine-Exons model. Positively weighted scaffolds in the Eponine-Exons model. Motifs that together form a scaffold are linked by lines. Scaffolds are generally composed of 1, 2 or 3 motifs. The black filled areas show the relative position distributions (histograms) of the motifs within a scaffold, while the sequences represent the most likely base at each position in the weight matrix of the motif.