The CNS Viewer software displays the bl2seq results of an orthologous pair of ferredoxin3 genes aligned on their start codon. The CNS repeats in the 5′ region of maize have been shown to be in a 5′ UTR intron (Nakano et al. 1997). The text boxes permit quick input to other applications, such as BLASTX or ORF predictors. The button “Remove/Display CNS Annotation” brings up the CNS list with the option to toggle “off.” Once off, a CNS does not appear in the graphic, but the data remain. The dark blue box denotes the experimentally verified exon in maize. The light blue box denotes orthologous space between the rice 5′ATG and the stop.
