using TREEMM for identification of bipartite motifs in promoter sequences

Question

[madhujamano]

Hi, I wanted to use TREEMM on a set of promoter sequences for their clustering and identification of sigma factor binding sites. I was able to run the algorithm and got the output that gave the motif number associated with the promoter sequence. But I don't know if I can assign the same sigma factor to that particular motif as predicted in Nicholas et. al, 2012, as I'm working with the same bacteria Bacillus subtilis. if anyone has used it, please help me with this.

Thank you