I'm afraid you may have to get creative if you want a full seal since there is a much larger gap at the top of the gate than the bottom. When I sealed mine with the Retraxx bed cover weatherstrip kit, I ended up with large gaps near the top. I don't know who supplies their seals but you may want to call and ask or just browse google for automotive weather strip, good luck.
This is how I sealed the sides (I didn't want to seal the bottom). Purchase a length of aluminum angle (1.5" wide per leg). Saw to length and notch at the top of the bed rails. Bond to the bed with silicone. This will still leave a small gap at the outboard upper ends which can easily be filled with silicone. Now a length of thin peal and stick weatherstrip can be attached to the angles to seal against the tailgate. This can all be purchased at most hardware stores.
I was able to get a good seal with the ExTang seal, looks similar to the Lund one offered by Truck Stuff above. You have to get a little creative with the gaps near the top, but if you take your time, you will find it 100% waterproof.
I have a BakFlip Cover and created myself a problem and did not realize it for awhile. The fit was a bit tight between the top of my tailgate and the Cover. The Tailgate seemed to shut and latch OK, but it wasn't. It opened up every once in awhile, cost me a Small Cooler one time, and some Halloween Pumpkins another time. Eventually fiddled with it and realized I wasn't hearing same "click" it used to have. Duh! Removed strip at top and all is well. It was always OK if Locked, but if not locked, oooppps.