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Finally got it to work like everyone else's!! Ok so it seems as though the mid-piece had some issues. I confirmed the primer sequence for amplifying the midpiece and did an experiment to test between what I had been using this whole time and a newly amplified midpiece fragment. The new ones came out almost flawless! =)
So I think the lesson is that even if people in the lab have done it a thousand times, make sure you understand the method thoroughly and double check everything that is handed down to you.
