Harbaugh led the Wolverines to 10-3 season, capping it off with an impressive 41-7 victory over the Florida Gators in the Citrus Bowl.
Harbaugh replied to Kaepernick, giving thanks and wishing him the best in 2016.
Together, Kaepernick and Harbaugh led the 49ers to two NFC Championship games (2012, 2013 seasons) and a Super Bowl (2012 season).
This season, the 49ers are 4-11 with one final game left and Kaepernick was benched for QB Blaine Gabbert before being placed on injured reserve with a torn labrum in his left shoulder. He is scheduled to make $11.9 million in 2016 if he is still on the roster on April 1. That base salary is guaranteed for injury.
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