I would not want to say it could not possibly be a clot, but it can be so many other things that I would not assume the worst. Your neck could be out of alignment, or you could have some inflamation - even mild injury can cause this sometimes. You could also be suffering from sinus problems, as there are many cases where the pain is at the base of the skull. In any case, it is best to have the doc check you out. He/she could rule out the clot pretty easily. Good luck!