A covered Tight End is a Tight End with a Wide Receiver outside of him on the line of scrimmage. If you want a Tight End eligible for a pass, he must not be covered up by another player since the only eligible receivers are those with the correct number (not 50-79) who are either in the back field or the last men on the line of scrimmage. Therefore having a player outside of the Tight End on the line of scrimmage is "covering" him up. A covered Tight End is legal for run and pass as long as the covered Tight End is not going out for a pass.
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An uncovered tight end is a tight end who lines up at the line of scrimmage without having a defensive player lining up directly in front of them.
In addition, after the ball is snapped, it could mean a tight end who is not picked up by a defensive player and is able to run their route with out a defensive player near them on the field of play. When you see this happen it is typically called a "blown coverage".