Figure 11 shows how SMOTIF performs on the A. thaliana chromosome 1, while searching for the Copia retrotransposon. We study the impact of allowing 0, 1 or 2 missing components out of the 6 simple motifs in the Copia structured motif. Figure 11(a) and 11(b) show the effect of sequence segmentation on SMOTIF-1 and SMOTIF-2, respectively. The x-axis shows the length of the segments, whereas the y-axis shows the time. The rightmost end point on the x-axis shows the case when the sequence is not segmented. For these experiments we used the IUPAC pos-list approach. The different curves in each figure show the effect of 0,1, or 2 missing components. Both figures suggest the best segment length is 10,000 base pairs. At that segment length, sequence segmentation can speed up the search around 2 to 3 times for SMOTIF-1 (depending on the number of missing components) and 4 times for SMOTIF-2. In the following experiments, we use 10,000 as the default segmentation length.