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yWriter can show you whether you're over-using a word within a chapter or a scene. Select a chapter and click Window then Word Usage Count. This will save a log file to the folder 'Counts' inside the project path (the place where the YWP file is stored). Each chapter file will be saved as the chapter filename with _count.txt added onto the end. This file contains a sorted list of all words (even common ones).

For scenes, you can get a list of the top 20 words by usage within the editor. Just click Scene then Top 20 Words. This list doesn't include common words like AND, SAID, I, etc (since they'd probably make up the top 20 in most files!). Once you've seen the list, you might discover you've used the word THEN 44 times in a 1200 word scene. You can (then) press F3, enter THEN and show each occurrence within the scene, perhaps editing the sentences to say the same thing in a different way, removing the over-use of your favourite word.