Figure 2. Selecting informative tag classes based on the change in strand cross-correlation magnitude.

For each class of tag alignment quality listed in Table 1, the plots show the change in strand mean cross-correlation profile when this class of tags is considered together with the base class of perfectly aligned tags (25bp, no mismatches). Three plots correspond to tag classes (a) without mismatches, (b) with a single mismatch, and (c) with two mismatches. Informative tag classes improve cross-correlation (marked by *), and are incorporated into the final tag set. The y-axis gives the mean change in cross-correlation profile within 40bp around the cross-correlation peak (Figure 1d).