SMDesigner input/output. (A, left) Secondary structure drawn by R2R; (A, right) portion of alignment motif EEF1A2 in Stockholm format. The “#=GC SS_cons” is the line describing secondary structure. (B) The output is generated for all sequences from the alignment. (Left) Secondary structure with two types of mutations; (right) portion of output sequences for Seq2 from the alignment in A. The output sequences corresponding to all the input alignment sequences are contained in the same FASTA file. The stars mark the base pairs located at the center of the stem chosen for mutation. The “mu1” is the disrupted mutant with the broken base pairs, and the “mu2” is the mutant with the restored base pairs. The boxed red nucleotides are altered nucleotides according to the mutation types.
