Table 1. Summary of secondary structure predictions.

Prediction number	Software	Method	Comparative	SHAPE data	Max. contact distance = 600 nt
1	RNAstructure	Thermod.	NO	YES	YES
2	RNAstructure	Thermod.	NO	NO	YES
3	PPfold 3.1	SCFG	YES	YES	NO
4	PPfold 3.1	SCFG	YES	NO	NO
5	GTfold (Aug 2011)	Thermod.	NO	NO	NO
6	GTfold (Aug 2011)	Thermod.	NO	YES	NO
7	GTfold (Aug 2011)	Thermod.	NO	NO	YES
8	GTfold (Aug 2011)	Thermod.	NO	YES	YES
9	UNAfold	Thermod.	NO	NO	NO
10	UNAfold	Thermod.	NO	NO	YES
11	PETfold	Combin.	YES	NO	NO
12	RNAalifold	Thermod.	YES	NO	NO
13	PPfold 3.1	SCFG	YES	YES (re-normalized)	NO

Prediction 1 is identical to the structure published in (7). In SHAPE-driven predictions, unless otherwise indicated, the SHAPE data published in (7) were used without re-normalization. The details for re-normalization used for prediction 13 are described in Supplementary Methods. In phylogenetic predictions, the manually curated HIV-1 alignment, described in Materials and Methods, was used. The full pairing schemes are provided in Supplementary Table S1.