Computational inference of putative functional elements in noncoding DNA sequence can significantly hasten the search for verified functional elements, such as transcription factor binding sites. However, while computational methods are able to identify promising putative elements, the number of regions of interest may remain unrealistic for experimental validation. Visualization of putative functional elements can assist tremendously in identifying the regions of greatest interest; interactive vizualization allows researchers additional means of asking and answering questions about putative elements. For example, interactive visualizations allow one to look at motifs in the context of verified functional elements or other putative elements, interactively altering the amount of information displayed and the level of resolution at which it is displayed. The work presented here describes initial efforts toward interactive visualization of putative junctional elements specifically for our work with conserved elements.