Login to cPanel, phpMyAdmin search, select the database, then click the ‘everything’ at the bottom of the page, and then in the drop-down menu in the middle of the page (see image below), select ‘Optimize Database’ . And you did.
Other way is to do it with plugin http://downloads.wordpress.org/plugin/optimize-db.zip from yoast.com as this plugin runs an optimize table command on your WordPress tables, effectively defragmenting it. This is very useful for tables that are frequently updated.
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