1. Plan A
   Use ClustalW to align the two tRNA sequences. Then fold the resulting alignment with RNAalifold.
   
   
2. Plan B
   Simultaneously align and fold the two sequences with Foldalign.
   
   
C
3. Plan C
   Structurally align the two MFE-structures computed by RNAfold with RNAforester in multiple mode (you would not get a consensus structure in pairwise mode). Are there any differences to the alignments from A. and B.?
   
   
4. Plan D
   Take these 20 tRNA sequences, extracted from Rfam, in multiple Fasta format. Use MatrixPlot to compute the mutual information. Can you detect the clover leaf in the plot?
   
   

Which plan works best? Which is the fastest one?