Then install something to run queries directly on the server. It doesn't have to be PHPMyAdmin or Adminer, you can make you own script in PHP or whatever language you use, it's very simple, for example a web form with a textarea and then the script should run the query and time the result at least to a millisecond precision. If you use any desktop program to connect to MySQL then the connection latency will be measured too and for faster queries the measurements will not be accurate enough.
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