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By default, only words longer than three characters are counted. This skips "the", "and" "a", and other common words that you probably can't change. The minimum size can be set in the General Preferences dialog.
Left click over a word in the popup will highlight all occurrences of that word in the text window.
Control-Left click over a word in the popup will highlight and view the next occurrence of that word in the text window.
Double-Left click on a word in the popup will display a list of synonyms.
The Find Synonyms button will also generate a list of synonyms. This is useful to find synonyms for a base word when a derived word is overused.
For example, use Find Synonyms to find synonyms for "discover" when "discovering" is overused.