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I am using preview latex in auctex. When you are inside an equation there is a blue background around the latex you are previewing, which means I cannot see the highlighing from transient mark mode. The highlighing from transient mark mode and preview latex are different colors so I do not believe this is a color conflict. How can I disable this?

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Delete the line (overlay-put ov 'face 'preview-face) from the function preview-toggle in preview.el.

In more detail, use M-x find-function preview-toggle (C-h C-f) to navigate to the relevant function, copy its contents into your init file, and delete the line that I mentioned. Alternatively, use override advice.

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