The ScanFold approach defines specific motifs of likely function. All predicted motifs containing at least one base pair with an average Zavg < -1 have been modeled, annotated, and compiled into individual PDF files for easy viewing.
Additionally, each of these motifs has been queried (using the Incarnato lab's cm-builder script) against ~25K coronavirus genomes using the Eddy lab's Infernal program in order to generate covariation models of the given motif. The resulting covariation model stockholm alignments were then tested using the R-scape program for evidence of statisitcally significant covariation. Here base pairs with significant covariation (GTp test; E < 0.05) are highlighted in green.
Results for experimentally informed motifs:
Full cm-builder/Infernal/R-scape/CaCoFold Results: