A miss fire.....my Evergreen is doing the same thing. Hopefully yours isn't doing it for the same reason mine is.
A way to figure out which cylinder it is -- Have someone hold the car in Drive while you listen to the thumping noise. Individually unplug each injector connector (one at a time, replugging back in when done) until you notice NO change in the thumping noise. Once you find THAT cylinder then you'll know which one is have the misfire. You will notice a distinct change in the idle/sound of the engine on the cylinders that are working fine, then when you get to the culprit cylinder, you'll notice NO change. Once you find THAT cylinder....start diagnosing. If you're good at the sound test, you can swap the coils/wires (depending on year) to the adjacent cylinder. Re-test using the sound check and if the misfire moves, then you know you have a bad coil/boot/spark plug wire.
Hope this helps....