2007 Chevy Cobalt Motor only sparking on two cylinders

I recently ran into some water on my car which my car stalled out. I've cleaned the entire motor of water and oil. I have good compression and my spark plugs are new but I don't get a spark on the #1 and #4 cylinder. I've checked the coilpacks and they all work fine. Could the ecu be messed up? It does show that there is A cel but when I go to scan for codes it tells me that there are no codes.