Figure 4.

Alignment of unique Class I sequences. The top 12 derive from the engineered library, whereas 10-32 is the lone class representative from the random library. The box contains the fixed 12-base central hairpin, with one or two extra base pairs in several of the sequences (as expected by chance). Bases that form Watson–Crick or G-U wobble pairs in the stems are underlined. The recognition loops are under the two heavy bars; bold text denotes 100% conserved bases, regular capital letters are semivariant bases (i.e., two species are allowed at that position), and lowercase are fully variable. The last base in the top strand of the outer stem, marked by an asterisk (*), is always a G or C, so it can also be considered semivariant.