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Does it feel like the car gets the hiccups?
At what speed is this most noticed at?
Any warning lights on or flashing?
Do all gears and shifts feel good?
You have described an ignition misfire here in this case and the flashing CEL also backs up that diagnosis. Most likely its just one or two coil on plugs failing and those effected ones need to be replaced as well as there spark plugs. A scan tool can be used to run a power balance test while this is occurring to see which cylinder(s) are having a concern.
This needs to be addressed SOON because this concern can cause catalytic converter failure which adds 1,000$ to the repair bill.