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Through most of Apple's history, Microsoft Office has had a tremendous market share in the Macintosh market. And Office is roughly as important to Microsoft as Windows. So it's not like Apple directly threatened Microsoft, at least not when Gates was the CEO.
Even in the pre-Macintosh era, Microsoft profited from Apple's success, due to Microsoft having written part of the operating system (Applesoft BASIC).
These companies have been complementary so often that Gates's remark isn't surprising.
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