SMOTIF Performance: Comparing SMOTIF-1 and SMOTIF-2. The figure shows how SMOTIF performs while searching for the Copia retrotransposon on Chromosome 1 from A. thaliana. (a) and (b) show the effect of sequence segmentation on SMOTIF-1 and SMOTIF-2, respectively. (c) and (d) compare the time and memory usage, respectively, for SMOTIF-1, when we use the recomputed or indexed full position recovery (e) compares the DNA versus IUPAC pos-lists for handling IUPAC symbols in SMOTIF-1. (f) shows the time for SMOTIF-1 and SMOTIF-2 on each of the 5 chromosomes of A. thaliana, with no missing components.