Table 6. Percentage sensitivity and positive predictive value (Sensitivity/PPV) for predicted base-pairs in the BRalibaseII benchmark.

	U5	g2intron	rRNA	tRNA
TKFST grammar	37.9/68.0	42.1/63.8	37.4/66.5	70.9/88.3
Stemloc grammar	74.9/73.9	64.3/56.7	51.0/59.0	74.0/76.4

We compared the performance of the TKFST model for structure-prediction accuracy during progressive multiple alignment of RNAs against the performance of a grammar with a richer model of RNA structure (Stemloc [18]). “g2intron” is the RFAM entry Intron_gpII, containing domains V and VI of the Group II intron.