You can optimize/repair your database via phpMyAdmin:
First, log into cPanel and open up the MySQL Databases section icon.
At the bottom of the screen, you will find a link for phpMyAdmin. Clicking on this link will open up a new browser window with the home screen for phpMyAdmin. On this screen, click Databases. This will list all the databases you have setup.
Click on the database you want to work on. The database screen will list the tables for the given database.
Click the Check All link on the bottom left. Then from the pull down menu choose Optimize /Repair Table.