The most common problem I've run into with applications slow performance is the lack of indexes on the databases. Sometimes this is just because the application ran fine with a small amount of data but now is working off a larger amount, or the application is being used in unexpected ways (running less 'common' queries run more often), or the production environment doesn't have the same indexes as the development environment or worse case the indexes were never created in the first place.
Without indexes queries can take seconds with indexes they take milliseconds!
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