One application of SMOTIF is to find structured motifs with long gaps. For example, we extracted the motif DNNNNDRYW [2578, 4202]RNNGVHVY, from the same 36 LTRs of A. thaliana mentioned above. Here we retain only the first and last conserved components in the resulting alignment of the 36 sequences. Note the relatively long gap ranges, with minimum gap l = 2578 and maximum gap u = 4202. SMOTIF was able to extract the approximately 83 million full positions, corresponding to 3 million start positions, in just 35.75s (SMOTIF-1) and 15.72s (SMOTIF-2).