I drive a Scion XA 20061

So this morning I drove to the store and everything worked just fine. I had no problems with my engine really running choppy that I noticed but when I got ready a few hours to go to work that is when I noticed something.

When I accelerated my engine would begin to kind of putter like it was having a problem shifting gears, my check engine light would flicker off and on and it happened when I accelerated usually around 50-60 MPH but a little bit in between too. I also noticed that when I would come to a stop light it would sound for a split second like it was going to cut off then kick back up like it was just catching itself.

When I went on my lunch I took it to Autozone to get them to run the diagnosis and the check engine light came on and stayed on my way. They told me the Diagnosis (Cylinder 1 Misfire P0301). I drove it home and it seemed to be working better than in the morning, still slight puttering but nothing horrible.

I ran it by the body shop and he had it in park and said it did not sound like it was running choppy in park so it would be harder to tell what it is....I honestly felt like he was trying to sell me a bunch of "possible" fixes but I wondered if anyone had a better idea of what this might be.

I greatly appreciate any insight anyone can give,
Thanks!