The search tool in IRESite is based on RNAforester package, currently part of Vienna RNA Package. The search is performed in the so called small-in-large mode of RNAforester. Your query structure is considered as the small one, the structures being searched within the database as the large ones. The small-in-large mode can be seen as performing global alignment of the small structure against local alignment of the large structure -- the algorithm tries to find the whole small structure within the large one.
Example of a search query
Table bellow shows first three hits against IRESite database. It shows
the text output of the database search and its graphical
representation. The right-most hairpin is the small structure, on the left
side is depicted the large structure in outline and detail
Black bases stand for identities, red bases within the small structure stand for gaps and gray bases in large structure are unmached regions between the two structure alignments.