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. Author manuscript; available in PMC: 2010 Jul 17.
Published in final edited form as: J Mol Biol. 2009 May 3;390(3):428–442. doi: 10.1016/j.jmb.2009.04.048

Figure 3.

Figure 3

Structure model for B. mori 5′ RNA (R2Bm). Structure is annotated for initial structural modeling constraints generated from strong (≥ 1/3 maximum intensity) or medium (≥ 1/9 maximum intensity) binding to oligonucleotide microarrays (boxed nucleotides), and from chemical mapping (green, blue, red, and orange circles, respectively, corresponding to strong reactivity, i.e. ≥ 6 times control intensity, with DMS, CMCT, NMIA, and CMCT or DMS overlapping with NMIA). Also annotated are base pair conservation (open boxes between nucleotides), compensatory mutations (filled boxes between nucleotides) and partition function probabilities (colored boxes or dashes between nucleotides). An annotation key appears on the figure.