If the first character on a line is 'p' or 'P', the line defines the width and decimal fields for the probability of the site. If the first character on a line is 'z' or 'Z', the line defines the width and decimal fields for the Z score of the site. If the first character is 's' or 'S' then the line defines a string to insert. This allows the user to put whatever they desire between the data items. Capital characters turn on the output.
Small characters turn it off.
Thus DfI turns on the data and scaninst files and leaves the scanfeatures off. The first character is defines how to normalize the reported Ri values. The Ri value at coordinate zero is called Ri0. The columns are defined in comments in the file. The matrix is searched over both the sequence and its complement.