Hi, I'm new in bioinformatics and I have had some trouble finding a binding site for a known transcription factor. To summarize, I'm interested in finding if any of my sequences (only 5 promoter sequences) have a certain motif, which has been reported for other similar organisms. I tried MEME discovery tool (web tool), but using just 5 sequences has given very weak results (e-values too high) which I guess are not reliable. I tried with FIMO and MAST using as input motifs some sequences reported in articles, but the results I got from both are quite different. For example, for one sequence that very likely has that motif, when using MAST I got at least 3 possibilities of the position of the motif, but when I use FIMO I got zero results.
Does anyone know what other tools can I use to confirm my results? Or do you have any advice on the strategy I can follow to find those motifs?
Thank you, and sorry for the long post!