1999 Jeep Cherokee Check Engine Light on and sometimes Flas

While driving to work, my check engine light came on and after I drove for about 10 miles the check engine light began flashing and the car engine began running very rough. The Check Engine light quit flashing and at red lights I would put the car in neutral and the engine would run smoother than if it was in drive. After, a few more miles of driving the engine began to run very smooth but the check engine light stayed on. What can this be?