STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species. CNS (Conserved Noncoding Sequence) is a short-sequence element that can regulate the transcription process. They inherit from a conserved evolution history. In grass species with closer relationship, closely homologous gene tends to more conserved in acting functions. The old common way to identify CNS are based on dual species, but it may cause more false positive. This tool added more species up to 6 to the analysis, and it could effectively remove CNSs that are less conserved. Combined this tool with transcriptomic data and genomic data analysis can help to speculate one of causal reasons to produce observed differences.