While capillary electrophoresis (CE) based sequencers are ubiquitous at most institutions, their application to quantitative nucleic acid structural characterization requires special expertise. We therefore set out to harness the potential of CE for the structural characterization of nucleic acids by quantitative chemical mapping. A major limitation to their adoption for nucleic acid structural analysis is the absence of software that can quantitate the elution trace. The ‘base calling’ algorithms necessary for sequencing are not suitable for quantification of the chemical and enzymatic mapping data necessary for structural analysis. Rather, an algorithm capable of deconvoluting overlapping signal is necessary along with software that transforms and manipulates the mapping data. To take advantage of high throughput CE sequencers, we have developed the experimental protocols and the Capillary Automated Footprinting Analysis (CAFA) software described available here that builds upon tested GE analysis tools. The structural analyses derived from CAFA based analysis will be a valuable addition to genome analyses.