Specific functions of ribonucleic acid (RNA) molecules are often associated with different motifs in the RNA structure. The key feature that forms such an RNA motif is the combination of sequence and structure properties. In this article, we introduce a new RNA sequence-structure comparison method which maintains exact matching substructures. Existing common substructures are treated as whole unit while variability is allowed between such structural motifs. Based on a fast detectable set of overlapping and crossing substructure matches for two nested RNA secondary structures, our method ExpaRNA (exact pattern of alignment of RNA) computes the longest collinear sequence of substructures common to two RNAs in O(H.nm) time and O(nm) space, where H < n.m for real RNA structures. Applied to different RNAs, our method correctly identifies sequence-structure similarities between two RNAs.