I have had considerable opportunity to experience what Legolas is talking about. As a Navigator in the USAF I would sometimes find myself on long overwater flights, well outside of the range of navigational aides, and unable to obtain a celestial fix because of overcast skies. I would sometimes get a feeling in the pit of my stomach that I was "off course" to the right or left and should alter heading even though I had no logical reason to do so. Over time I learned to trust those feelings and make the course change. I suspect that my "sub-conscious" was processing information that my conscious mind was not aware of and manifesting the result as a bodily "feeling". I developed quite a reputation in my Squadron for being able to navigate with limited navigational equipment.
A more interesting question regarding the "sub-conscious" is Where is the sub-conscious?