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MySQL same queries run much slower on migrated website.

I have recently registered a new domain under the same GoDaddy account and started splitting away parts of my old website under the new domain. Both websites use the same instance of a MySQL database, yet queries run very much slower under the new domain. files. To prove this I have even created 2  literally identical PHP  files using the same MYSQL queries, and connecting to the same DB  under both domains as below:

 

(1) olddomain.org/query_speed_comparison.php

(2) newdomain.org/query_speed_comparison.php

 

The first file takes 1 second to complete, while the second takes 10 seconds. The only difference is that the first PHP file is hosted on the public_html folder while the second is hosted in a public_html/newdomain.org subfolder (same that hosts the index.html of my new website). Is there anything I can do to improve the performance?

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