Figure 4.

Increased accuracy from alignment of tandem repeats. Plots show normalized Smith-Waterman alignment scores as a function of the number of repeats before (gray) and after (red) alignment. Before consensus sequence generation, alignment score exhibits no dependence on repeat count. Since each “before point” represents an average over all repeats in that read, the observed narrowing arises solely because the increased number of repeats decreases the standard deviation of the average alignment score. After the consensus sequence is generated, the alignment accuracy exhibits a strong dependence on the number of repeats used.