Employing the tools ClustalW, RNAalifold, RNAfold and RNAforester, this pipeline can improve structural conservation of RNA sequences within the twilight zone of 30 60% sequence identity. After constructing a consensus structure by alignment folding, plan AC* abandons the original sequence alignment, refolds structures individually, but restricted by the consensus, aligns the structures (irrespective of sequence) by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re submitted to alignment folding, etc...