Given several hundred candidate regulatory regions of about 100bp in human, what is the best method to locate orthologous regulatory regions in several other closely to medium-related species? The whole genome alignments on UCSC seem a good place to start but I'm not sure how confident I should be in their alignment of non-coding regions. What is the state of the art for this sort of alignment? I am happy to use many other species such as those in the 46-way UCSC alignment (http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/multiz46way/). I would like to minimise type I errors and be fairly conservative predicting orthologous regions.