The six-year veteran quarterback who drew particular attention and headlines last season by not standing for the national anthem, met with new general manager John Lynch and coach Kyle Shanahan before making the move.
Kaepernick made a meteoric rise with the 49ers under coach Jim Harbaugh, leading them to the 2012 NFC title and a close loss to Baltimore in the Super Bowl. But his career spiraled in recent seasons, and he was benched for journeyman Blaine Gabbert.
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His decision leaves the team with no quarterbacks on the roster. Gabbert and Christian Ponder also are free agents.
Kaepernick, 29, has indicated he plans to stand for the anthem next season.
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