Chip Kelly made a subtle comment that makes Colin Kaepernick's future with the 49ers sound more in doubt than ever

The San Francisco 49ers’ hiring of Chip Kelly was initially thought of as a win for Colin Kaepernick.

Kelly’s quarterback-friendly, read-option offence would seemingly work wonders with a young, athletic quarterback with a cannon for an arm.

However, in the months since the hire, the Kelly-Kaepernick union has been cast in doubt, as the 49ers explore trade options for Kaepernick. The Broncos and Browns have been named among the primary suitors.

On Thursday while talking to media, Kelly made a subtle comment that makes it sound like he’s not banking on working with Kaepernick, via Matt Barrow of the Sacramento Bee (emphasis ours).

If he’s here on April 4 we’re going to coach the heck out of him, and he’s going to work his (tail) off,” Kelly said.

April 4 is the beginning of the team’s offseason program.

As ProFootball Talk’s Mike Florio noted, this is a far cry from what Kelly was saying late in February.

“I don’t know what the narrative is that, ‘Is he on the team? Is he not on the team?’ It’s never been a question. I’m excited to work with Colin. I’ve never thought that, ‘Hey, I’m going to go to San Francisco and he’s not going to be there.’ … Kap’s really good. … You can just look at the tape and know how talented he is. Our job is acquiring talent, not getting rid of talent.”

During Kelly’s introductory press conference, he was strangely hesitant to speak about Kaepernick, raising red flags about the possibility of the two working together. However, the above comment seemed to put fears to rest that Kelly doesn’t want Kaepernick.

Of course, Kelly could have been covering for the front office, who may have wanted to deal Kaepernick all along. But for Kelly to say “if” he’s on the team does give some real indication that he could be on the move.

Kaepernick’s agents reportedly requested permission to seek a trade before the league’s new year opened, and again, reports say the 49ers have been talking to the Broncos and Browns about a trade. Kaepernick’s 2016 contract locks in if he’s on the roster after April 1.

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