Supplementary Material Four RNA families with functional transient structures

• The CM(covariation model) files built and calibrated from the curated alignments above are in folder CM files. For each family, the cm files for all alternative structures are included. However, the pseudoknotted hairpin is removed from both HDV ribozyme (the active structure) and SAM riboswitch (the SAM-bound structure) as Infernal does not handle pseudoknotted structure. In the active structure of HDV ribozyme, a 6-bp hairpin and a 2-bp hairpin located near the 5’ end, causing pseudoknot, are removed; thus, the cm file is made of the remaining active structure. In the SAM-bound structure of SAM riboswitch, a 4-bp hairpin causing pseudoknot is removed, and the cm file is made of the remaining SAM-bound structure.