Figure 3.

Suppressed secondary structure in coding region. This figure shows part of the CAPZA2 alignment in the coding region, before (top) and after (bottom) randomization. The original alignment is devoid of secondary structure, whereas the randomized alignment contains a small, hairpin-like structure which mostly involves newly formed base pairs between codon positions 2 and 3. Newly formed base pairs are underlined in pink, altered base pairs in green and broken base pairs in yellow. Real and potential base-pairing partners are shown in upper case letters. The consensus base pairs for RNA molecules, i.e. {G−C, A−U, G−U}, correspond to {G−C, A−T, G−T} on DNA level, as depicted here. See Results for a detailed discussion.