Table 1: Sequences used in the experiments

RNA	NSEQ	Reference Structure
		Organism	L (nt)	EP	EHLX	EK
5S rRNA	12	Escherichia coli	120	40	5	0
SRP RNA	12	Bacillus subtilis	271	78	14	1
Telomerase RNA-5'-end	9	Homo sapiens	210	50	5	1
tmRNA	8	Escherichia coli	362	106	12	4
16S rRNA	10	Escherichia coli	1542	478	67	2
HIV-1-RT RNA	1	-	35	11	2	1
TYMV-3'-end	1	-	86	24	5	1
TMV-3'-end-up	1	-	84	25	6	3
TMV-3'-end-down	1	-	105	34	6	2
HDV Ribozyme	1	-	87	28	4	1
Anti-genomic HDV Ribozyme	1	-	91	24	4	1
NSEQ: Number of sequences used EP: Expected number of base-pairs EHLX: Excepted number of helices EK: Expected number of psuedoknots. Only helices with length > 2 are counted.

5S rRNA are from the following species:
Escherichia coli,
Verrucomicrobium spinosum,
Empedobacter brevis,
Flavobacterium johnsoniae,
Borrelia burgdorferi,
Deinococcus radiodurans,
Thermus thermophilus,
Chlorobium limicola,
Pedobacter heparinus,
Herpetosiphon aurantiacus,
Synechococcus lividus,
Prochloron sp.

SRP RNA are from the following species:
Bacillus subtilis,
Listeria monocytogenes,
Bacillus brevis,
Brevibacillus brevis,
Clostridium perfringens,
Methanococcus jannaschii,
Methanococcus voltae,
Methanothermus fervidus,
Methanobacterium thermoautotrophicum,
Methanosarcina acetivorans,
Pyrococcus horikoshii,
Thermococcus celer.

Telomerase RNA are from the following species:
Homo sapiens
Geomys breviceps
Cavia porcellus
Mus musculus
Rattus norvegicus
Cricetulus griseus
Suncus murinus
Dasyurus hallucatus
Gallus gallus

tmRNA are from the following species:
Escherichia coli,
Haemophilus influenzae,
Aeromonas salmonicida,
Vibrio cholerae,
Pseudomonas aeruginosa,
Pseudoalteromonas haloplanktis,
Marinobacter hydrocarbonoclasticus,
Actinobacillus actinomycetemcomitans.

16S rRNA are from the following species:
Escherichia coli,
Aquifex aeolicus,
Aquifex pyrophilus,
Calderobacterium hydrogenophilum,
Hydrogenobacter thermophilus,
Bacteroides cellulosolvens,
Bacteroides distasonis,
Bacteroides eggerthii,
Bacteroides forsythus,
Bacteroides fragilis.