Aligning multiple genomic sequences is becoming widely accepted as a powerful mechanism for identifying important functional regions such as regulatory elements. MultiPipMaker (http:// pipmaker.bx.psu.edu/pipmaker/; Schwartz et al. 2003 ) and mVISTA (http://gsd.lbl.gov/vista/index.shtml; Bray et al. 2003; Frazer et al. 2004 ) are two of the most popular web servers that conveniently combine alignment engines with visualization capabilities. MultiPipMaker, and a new server zPicture (http://zpicture.dcode.org/; Ovcharenko et al. 2004) , use the local alignment program BLASTZ as their alignment engine (Schwartz et al. 2000) ; VISTA uses AVID, a global alignment program (Bray et al. 2003; Frazer et al. 2004 ). Local alignment tools find high-scoring, short matching segments and extend these regions based on a scoring threshold. Local alignments may permit greater diversity between sequences by finding regional similarities. Segments of similarity need not be conserved in order or orientation. This feature may be advantageous for finding conserved transcription factor binding sites, which are very short and prone to reordering (Bray et al. 2003) .