FIGURE 5.

QuShape analysis by reference. An automated sequence alignment of TPP riboswitch RNA traces is shown. Sequence alignment was achieved by aligning experimental traces [(+) and (−) reagent] with a sequence trace from an independent experiment. The ddNTP and (+) and (−) reagent traces from the reference experiment are drawn in light colors. Because these experiments were performed under different conditions, many nucleotides exhibit distinctly different fluorescence intensities in their (+) reagent traces; nevertheless, QuShape completed the reference-based analysis of this experiment in <1 min without error.