Table 1.

RNA Families Tested

Name	Length			MFE acc.
	med	min	max	med	min	max
tRNA	75	73	77	0.51	0.00	0.95
5S rRNA	120	119	122	0.55	0.15	0.85
RNaseP	327	205	354	0.49	0.13	0.68
Intron group I	543	480	554	0.30	0.06	0.74
16S rRNA (small)	958	940	969	0.25	0.14	0.45
16S rRNA (med)	1259	1231	1399	0.29	0.17	0.37
16S rRNA (long)	1537	1528	1548	0.41	0.18	0.64
16S rRNA (extra)	1962	1841	2090	0.34	0.18	0.42

The RNA families tested were chosen to span a range of lengths. The data on tRNA, 5S rRNA, and 16S rRNA families were taken from the Comparative RNA Website (51), the data on RNaseP from the RNase P Database (52), and the data on intron group I from Rfam (53). Each family is represented by five sequences that span the available spectrum of MFE accuracies, as calculated by F-measure. The 16S rRNA sequences were subdivided based on length into four categories roughly 300–400 nucleotides apart, as this is the spacing for the two prior families: sequences in the “small” category are ∼950 nucleotides long, those in the “medium” category ∼1250, those in the “long” category ∼1550, and those in the “extra long” category ∼1950. This table provides the median and minimal and maximal lengths and MFE accuracies of the five sequences in each family. Further sequence information can be found at the end of the article in Table 2.