Score calculation and prediction of RNA editing. The hypothetical alignment shows an input sequence aligned to three homologues from the Aligned Sequence Database. The predicted state is boxed. Column 1 shows a case where RNA editing is not possible. Column 2 presents a case where the editing state is more strongly supported. Column 3 demonstrates the various rules placed on the algorithm. The CUG is taken as the correct state because it requires fewer edits than UUG and is edited at the second position, whereas UCG is edited at the first position.