In my older version of Toad, there was an option to choose a destination schema when doing a compare schema. I am on Toad for Oracle 10.6.1.3 now and do not see that option anywhere.
In Toad for Oracle 10.6.1.3, the GUI for choosing destination has been removed. Instead you can click on the Plus sign button located on the right hand side to "Add Target Schema" to compare.
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