Modified from Ouvard et al. (2000).
A right-handed double helix composed of a succession of complementary hydrogen-bonded nucleotides between paired strands.
Unpaired nucleotides separating helices.
Helix closed distally by a loop of unpaired nucleotides (terminal bulge).
Succession of unpaired nucleotides at the end of a hairpin-stem loop.
Succession of unpaired nucleotides on one strand of a helix.
Group of nucleotides from two antiparallel strands unable to form canonical pairs.
Subsequent mutation on one strand of a helix to maintain structure following initial mutation of a complementary base.
A single insertion of a nucleotide relative to the rest of the multiple sequence alignment.
A single deletion of a nucleotide relative to the rest of the multiple sequence alignment.
An ambiguous position within a multiple sequence alignment that cannot be described as an insertion or deletion. RAAs, RSCs, and RECs are all examples of indels.
Two or more adjacent, non-pairing positions within a sequence wherein positional homology cannot be confidently assigned due to the high occurrence of indels in other sequences.
Region involved in base-pairing wherein positional homology cannot be defended across a multiple sequence alignment; inconsistency in pairing likely due to slipped-strand mispairing.
Variable helical region flanked by conserved basepairs at the 5' and 3' ends, and an unpaired terminal bulge of at least three nucleotides; characteristic of RNA hairpin-stem loops.