Figure 6

The footprints of Algorithm 2 plotted in the xy -plane. These are frames that are visited by Algorithm 2 during its search for the bubble stitches (filled yellow). The frames are located in a band along the diagonal, suggesting that the search space is proportional to sequence length. Grid frames below the diagonal (grey) are skipped. Grid frames crossing the diagonal (red) are broken into fractal frames (blue). The bubble stitches (filled yellow) are those grid frames above the diagonal (green) and fractal frames (blue) that have p_v(a, b) ≥ p _c . Frames with side lengths below 20 bp are not shown to unclutter the figure.