Alignment consistency. A violation of RNA structural alignment consistency is shown (left), together with a possible correction (right) – see text for details. Note that the inconsistent alignment may maximise sequence similarity, showing 3 mismatches versus 1 mismatch and 2 indels, with the concrete outcome depending on the gap scoring used. Inconsistency is the reason why it is dangerous to align two structures in string representation by a standard sequence alignment algorithm. Inconsistency is hard to detect by human eye inspection, and structural alignments in databases are not always free from consistency violations.