Figure 4.

(A and B) Structural RNA logo analysis of the hairpin loop. Two different common loops were detected in position 493–501 in the multiple alignment file: seven bases long (((…….))) and five bases long (((…..))). By composing a correct regular expression pattern for each loop, removing the gaps and including 16–17 bases expanding from each side of the loop, we were able to distinguish between 83 large loop RNA structures and 21 small loop structures. All alignments were analyzed by structural RNA logo analysis. The results are presented in bits, reflecting the information content of each base. The base pair fraction of each position has been calculated and appears below the logo. (A) refers to the large stem–loop structure and (B) refers to the small one. (C and D) Protein logo analysis of the amino acid sequence encoded by the β3/β4 hairpin loop region. The two nucleotide data sets (large and small loop), described in (A) and (B), were translated to amino acid sequences and analyzed by protein logo analysis. The results are presented in bits, reflecting the information content of each amino acid. (C) Refers to the large loop hairpin sequence and (D) refers to the small loop hairpin sequence.