Have you looked whether any published ChIP-Seq datasets for STAT6 show binding to these gene loci (e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190958/ or http://www.sciencedirect.com/science/article/pii/S1074761310002141)? Eventhough these studies did not look at macrophages per se, some sites may be conserved across cell types, so it is a good starting point. Probably higher yield that trying to map a candidate STAT consensus motif to these genes.

Daniel rised a Great Point!

But another Thing would Might be the case is that the binding sequence can be a Bit Variable (like with other Factors).

Maybe your program cannot find the Site because of that.

But because of the Chip Experiment i would say that your factor should bind in a specific Region.

Just Analyse by Hand this 200-500bp if stat6 could bind.

All the best,

Sebastian

Go to http://zpicture.dcode.org/ Paste your gene sequence (e.g your promoter region) in both the sequence box (sequence 1, sequence 2) in fasta format. Press submit. Then press rVISTA in the rVISTA 2.0 portal tab. In the next page leave the vertebrates option ticked and press again submit. In the next page select your transcription factor (e.g STAT6) and press submit. Then you can check the alignment of predicted STAT6 binding sites on your sequence... hope that helps!!

Another way is to use the tool in the website ECRBROWSER. you select the gene in which you are looking the binding site in, then you will see highlighted in its sequence the regions of the genes conserved within species. You will have to select each time a different region and look for the binding site in it using either already selectable matrices or inserting your own matrix