A modification of the basic SLiMFinder tool to specifically look for SLiMs shared by a query sequence and one or more additional sequences. To do this, SLiMBuild first identifies all motifs that are present in the query sequences before removing it (and its UPC) from the dataset. The rest of the search and stats takes place using the remainder of the dataset but only using motifs found in the query. The final correction for multiple testing is made using a motif space defined by the original query sequence, rather than the full potential motif space used by the original SLiMFinder. This is offset against the increased probability of the observed motif support values due to the reduction of support that results from removing the query sequence but could potentially still identify SLiMs will increased significance.