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The color-coded Index Analysis feature highlights missing indexes as well as shows which indexes are used and which are not used in the default execution path. The Index Analysis feature highlights issues where the database optimizer might not be using the preferred indexes. SQL Query Tuner also lists indexes on the tables that do not have fields in the WHERE clause helping the designer to see if adding an additional predicate in the WHERE clause might make use of an existing index.

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The layout of the Analysis tab shows the SQL text and Visual SQL Tuning (VST) diagram on the top and the indexes on the tables in the query below. 

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Automate SQL tuning and profiling with SQL Query Tuner.
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