The phylogenetic footprinting program TRACKER [41] was designed specifically to search for conserved non-coding sequences in large gene clusters. It is based on a similar philosophy as segment based alignment algorithms. The TRACKER program computes pairwise local alignments of all input sequences using BLASTZ [42] with non-stringent settings. BLASTZ permits alignment of long genomic sequences with large proportions of neutrally evolving regions. A post-processing step aims to remove simple repeats recognized at their low sequence complexity and regions of low conservation. The resulting list of pairwise alignments is then assembled into clusters of partially overlapping regions. Here the approach suffers from the same problem as DIALIGN, which is, however, resolved in a different way: instead of producing a single locally optimal alignment, TRACKER lists all maximal compatible sets of pairwise alignments. For the case of Figure 1(C), for instance, we obtain both M2M3 and M2M3. Since this step is performed based on the overlap of sequence intervals without explicitly considering the sequence information at all, TRACKER is very fast as long as the number of conflicting pairwise alignments remains small. In the final step DIALIGN is used to explicitly calculate the multiple sequence alignments from the subsequences that belong to individual clusters.