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Kaepernick had a miserable 2015 season that saw him get benched for Blaine Gabbert, but he'd seemingly be a perfect fit for Kelly.
In Kaepernick, Kelly would have a quarterback capable of running his read option, with the speed to carry the ball himself and the arm to hit targets all over the field.
However, according to a report from Manish Mehta of the New York Daily News, Kaepernick wants out of San Francisco and wants to join the Jets.
Mehta reports that the Jets are "aware and intrigued" by Kaepernick's desire to play for them, but don't want to reach out for fear of tampering.
Mehta writes:
Although Kaepernick wants to play in New York, he still has five years remaining on a blockbuster $114 million extension signed in 2014 that includes escape hatches for his current employer. The Jets, coming off a 10-win season, would have to trade for Kaepernick or wait until he's cut.
The 49ers must make a decision to keep, trade or cut Kaepernick before April 1 when his 2016 base salary of $11.9 million becomes guaranteed. San Francisco would save $8.5 million by cutting Kaepernick, who is scheduled to have a $15.9 million cap charge this season.
The report is interesting for the Jets, who, with a stingy defense and deep offense, could become a true contender with Kaepernick at the helm.
For the 49ers, however, it becomes a complicated situation. Chip Kelly caught the NFL world off guard when he was noncommittal about Kaepernick during his introductory press conference, saying it was against league rules to talk about players at this point in the offseason. His comments raised flags, though in fairness to him, he also didn't talk about other players on the 49ers.
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Nonetheless, the NFL world began to wonder if Kelly even wanted Kaepernick in the first place, which would come as a surprise. Around the time of Kelly's hire, there were reports that Kelly had been figuring out a way to get Kaepernick. Once he signed with the 49ers, that pursuit was over.
If Kelly isn't interested in working with Kaepernick, it makes his hire a bit puzzling. The 49ers are facing a lengthy rebuild, and though there are some intriguing pieces for Kelly to work with, Kaepernick was seemingly the prized asset - the player Kelly could rejuvenate to give the 49ers a boost.
That Kaepernick is still under contract makes the entire situation even more fascinating. If Kaepernick really wants out, he can force the 49ers' hands to a certain extent, but it will say a ton about Chip Kelly and his tenure with the team if they decide to cut, trade, or keep Kaepernick in the coming months.