Stephen Hill runs for a third-quarter touchdown at MetLife Stadium....

Stephen Hill runs for a third-quarter touchdown at MetLife Stadium. (Sept. 9, 2012) Credit: Jim McIsaac

Rex Ryan stopped short of officially ruling out Stephen Hill for Sunday’s game against the 49ers, but it’s all but certain the rookie wideout won’t play.

“I would say, you miss the first two days of practice, I would say he’s doubtful,” the Jets coach said Thursday morning, shortly after announcing Hill would sit out practice for the second straight day.

The wide receiver suffered a hamstring injury in their Week 3 win over Miami and though he did return to the game, he hasn’t practiced since.

The rookie, who suffered the same hamstring injury at the end of OTAs, told reporters Wednesday that he hasn’t undergone any tests.

Should Hill be forced to sit out,  Chaz Schilens and Jeremy Kerley would get more snaps, said Ryan.

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Though the Jets likely will be without their deep-field threat, it sounds as if TE Dustin Keller (hamstring) will be able to play after missing the past two games. Though hs backup, Jeff Cumberland, has “filled in pretty nicely for him,” said Ryan, the coach also admitted “there is a difference” when Keller’s not on the field.

“You’re talking about one of the premier receiving tight ends in the league,” said the Jets coach. “And he’s competitive as a blocker, so those guys are hard to replace.”

Ryan said having Keller available “maybe” gives him and the coaching staff the opportunity to use both tight ends on the field at the same time. “We’ll see,” he said. “Hopefully Dustin will be out there. I assume he will be.”

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Barring any setback, Keller is expected to be limited in practice today – along with LB Bryan Thomas (hamstring), WR Patrick Turner (hamstring) and S Eric Smith. Ryan said Smith, who did not practice Wednesday, is on a similar alternating practice schedule as S LaRon Landry (Achilles, foot).

Speaking of Landry, he will not practice Thursday due to his pitch count, and neither will Hill.

LB Bart Scott (hyperextended toe) may or may not practice, according to Ryan. Same is true with FB John Conner (knee). Scott did not practice Wednesday and Conner was limited in practiced that day.

If Thomas is healthy enough to face the 49ers, he’ll start at OLB. In his absence the past two week, backup Garrett McIntyre registered two sacks in Pittsburgh and two tackles and a pass defensed against Miami.

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