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The problem could be that the engine is running rough or it could simply be a vibration.
If it's running rough there are a few things remaining.
It could be an injector issue. If you have one or more injectors that are leaking or not spraying enough then it will cause the affected cylinders to miss. If you can identify what cylinders are running poorly then you can swap those injectors with good cylinders and see if the miss moves.
The problem could also be carbon buildup in the cylinders and on valves. A fuel system cleaning or top end cleaner ran through the engine will make a difference if this is the case.
It could also be loss of compression on one or more cylinders due to valve sealing issues, ring wear, broken valvespring, or a cam or lifter issue.
If it's actually a vibration rather than the engine running rough then it could be a broken flexplate, bad crank damper or an out of balance engine accessory.