TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
So databases like TRANSFAC are of somewhat... variable quality. Those matrices maybe have been derived from a program that just doesn't output a count matrix, but instead outputs a frequency matrix directly. What I would do, and what i have seen people do in published papers, is just multiply the matrix by 100 and round down. It's a kludge, but you'd better be quality checking the matrices somehow anyway, otherwise you're going to get 90% crap.