Figure 1.

An example RNA sequence family. Top: a toy multiple alignment of three sequences, with 28 total columns, 24 of which will be modeled as consensus positions. The [structure] line annotates the consensus secondary structure: > and < symbols mark base pairs, x's mark consensus single stranded positions, and .'s mark "insert" columns that will not be considered part of the consensus model. Bottom: the secondary structure of the "human" sequence.