(CNN) — Former FBI Director Louis Freeh’s investigation into possible wrongdoing at Penn State University appears to be examining football coach Joe Paterno’s apparent preference for handling scandalous issues internally, and what role that may have played in a potential cover-up involving former defensive coordinator Jerry Sandusky, convicted on 45 counts of child sex abuse on June 22.

Freeh’s group has been poring over internal Penn State e-mails and has interviewed a past university official about the way Paterno influenced a variety of disciplinary matters, according to a source with knowledge of the investigation. Freeh is leading an internal review of Penn State’s handling of the scandal that is unrelated to criminal investigations.

The e-mails obtained by CNN from a source familiar with the investigation, and first reported by the Wall Street Journal, show Paterno wielded power that went well beyond the realm of football or even the athletic department.

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