A position I want more popped up after I applied to a different one...

Yesterday I applied to a company I would like to work for and it was for a position that I felt that I was qualified for, but it wouldn't have been my first choice. Today I got an email from LinkedIn with suggested jobs and that same company posted a job today that is exactly what I'm looking for.

I've heard the advice not to apply to multiple positions within the same company, so what do I do? Would submitting another application hurt my chances? I could always address the multiple applications in my cover letter if that's an option.

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