RNA design is a major challenge for the future development of synthetic biology and RNA-based therapy. The development of efficient and accurate RNA design pipelines is based on trial and error strategies. The fast progression of such algorithms requires assaying the properties of many RNA sequences in a short time frame. High throughput RNA structure chemical probing technologies such as SHAPE-MaP allow for assaying RNA structure and interaction rapidly and at a very large scale. However, the promiscuity of the designed sequences that may differ only by one nucleotide requires special care. In addition, it necessitates the analysis and evaluation of many experimental results that may reveal to be very tedious. Here we propose an experimental and analytical workflow that eases the screening of thousands of designed RNA sequences at once. In particular, we have developed shapemap tools a customized software suite available at https://github.com/sargueil-citcom/shapemap-tools .