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Does it mean "MicroTech was outside Auburn City" or "besides his time for studying at Auburn college, he ran MicroTech?"

"For eight years Zalik ran MicroTech Information Systems out of Auburn, Alabama. Like many tech success stories, Zalik was so successful so soon, he eventually dropped out of Auburn. In 1996 he sold the company, moved to Atlanta and founded two more companies — Phoenix and Outweb — using the MicroTech sale proceeds, which numbered "in the millions," Zalik told Bloomberg last year. (He actually first invested the proceeds in commercial real estate, a well-timed bet, before founding the additional companies.)"

Source: CNBC

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It may seem contradictory, but it's actually closer to in than either of your guesses. To say a company was run out of a place is to say that the company is:

  1. located in that place
  2. services customers outside that place

You'll often hear this phrase used when referring to a corporation's headquarters; while that corporation may officially be based in one location they service customers nationwide if not globally.

In this case, Zalik's company was located in Auburn, and likely serviced customers both in and out of Auburn, successfully enough that he eventually had to leave to grow his business.

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