We evaluate our algorithm by extracting the conserved features of known transcription factor binding sites in yeast. In particular we used the binding sites for the Zinc (Zn) factors [11]. There are 11 binding sites listed for the Zn cluster, 3 of which are simple motifs. The remaining 8 are structured, as shown in Table 5. For the evaluation, we first form several structured motif templates according to the conserved features in the binding sites. Then we extract the frequent structured motifs satisfying these templates from the upstream regions of 68 genes regulated by zinc factors [11]. We used the -1000 to -1 upstream regions, truncating the region if and where it overlaps with an upstream open-reading frame (ORF). After extraction, since binding sites cannot have many occurrences in the ORF regions, we drop some motifs if they also occur frequently in the ORF regions (i.e., within the genes). Finally, we calculate the Z-scores for the remaining frequent motifs, and rank them by descending Z-scores. In our experiments, we set the minimum quorum threshold to 7% within the upstream regions and the maximum support threshold to 30% in the ORF regions. We use the shuffling program from SMILE [14] to compute the Z-scores. The shufffing program randomly shuffles the original input sequences to obtain a new shuffled set of sequences.