NRMP question

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Because categorical spots and advanced spots at the same university use different program #'s, it looks like they will be counted separately when costs add up. I say this because when I went to the NRMP website to fart around and practice making my rank list, it did in fact list them separately. That is, Program A was listed twice, making it my # 1 and # 2 choice. I don't think the software accounts for the fact that #1 and #2 are actually at the same program. Anyone hear differently?
 
If a program has both categorical and advanced positions available, then you will rank them as two separate choices and not necessarily consecutively (i.e either #1 and #2 or #1 and #5 etc). I ranked 9 programs and filled up 15 spots on my ROL.
Good luck
 
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