Are there any glaring holes in my app or would I be competitive?

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You should be fine... There are multiple MD/PhD (including MSTPs) who will be interested in you. However, you need to apply broadly with 10 reach, 10 match, and 5 near you (state/non-MSTP). Your CARS score will diminish enthusiasm of the reach schools... but your pubs and MS will be very helpful. PM me if you want to discuss your list more privately.
 
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