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I have a VPS with three accounts and 5 db's. Recently I added MySQLTuner. All of my tables are MyISAM, but the results MySQLTuner are showing that I have 14 tables that use InnoDB.

[--] Data in MyISAM tables: 257M (Tables: 618)
[--] Data in InnoDB tables: 560K (Tables: 14)

I looked all of my databases on phpMyAdmin and I couldn't find those tables.

Is there any way to find them?

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Login as root@localhost and query information_schema.tables by Storage Engine

SELECT table_schema,table_name
FROM information_schema.tables
WHERE engine='InnoDB';

To locate the InnoDB tables that are belong to you, run this

SELECT table_schema,table_name
FROM information_schema.tables
WHERE engine='InnoDB'
AND table_schema NOT IN
('information_schema','performance_schema','mysql');

GIVE IT A TRY !!!

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