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First read the terminology for a rna cycle. A stacked helix is a run of helices, 5′ to 3′, connected by cycles that have 1 entry helix and 1 exit helix. In the e.coli 5S example the helices at 16, 18, 28, and 31 form a stacked helix. A stacked helix doesn’t necessarily imply that they are visually aligned. A stacked helix may end in a hairpin loop helix.
