Non-coding RNAs (ncRNAs) show a unique evolutionary process in which the substitutions of distant bases are correlated in order to conserve the secondary structure of the ncRNA molecule. Therefore, the multiple alignment method for the detection of ncRNAs should take into account both the primary sequence and the secondary structure. Recently, there has been intense focus on multiple alignment investigations for the detection of ncRNAs, however, most of the proposed methods are designed for global multiple alignments. For this reason, these methods are not appropriate to identify locally conserved ncRNAs among genomic sequences. A more efficient local multiple alignment method for the detection of ncRNAs is required.