Table 1. Sensitivities of pairwise SHAPE-dependent sequence alignments relative to accepted alignments.

Sequence 1	Sequence 2	Sensitivity relative to CRW alignments (%)
		Nucleobase identity	SHAPE-only	Combined SHAPE and nucleobase identity
				Pairwise	MSA
E. coli 16S	C. difficile 16S	84	83	94	94
	H. volcanii 16S	72	71	89	92
E. coli 23S	C. difficile 23S	83	73	94	95
	H. volcanii 23S	58	41	76	79

SHAPE-only sequence alignments did not use sequence information. Accepted alignments are from the CRW [11]. Nucleobase identity-based alignment used the Needle algorithm [14] on the EMBOSS server [15] with default parameters. For predictions incorporating both SHAPE reactivities and nucleobase identity, sensitivities are given for both pairwise comparisons and for multiple sequence alignments (MSA) generated by T-Coffee [16].