This is a variation of the typical question of "How can I find common motifs in my sequences?", that is usually answered by using MEME Suite.
In this case, I have 4 DNA candidate sequences (all of the same length), and I am interested in finding any possible TF binding site motif that may be in them. These sequences are all independent, so I am not interested in finding anything in common between them.
I have tried CentriMo, tool of the same suite, versus some databases such as JASPAR, but I didn't had success, and I am afraid that maybe it does not work like that, or that maybe, with these sequences, the e-value is too low for it to select a hit. Am I doing something wrong? Should I use another tool?
Thank you very much to you all.