SANTA CLARA — Colin Kapenerick downplayed the six delay-of-game penalties he and the 49ers’ offense have been assessed this season, citing how they’re a “minor” blip in their overall methodology.

Same goes, he said, for their early usage of timeouts.

But play-clock issues, in particular, seem to have plagued the 49ers throughout this season, not to mention last season, when Kaepernick and Alex Smith each took four delay-of-game penalties.

“I feel like it’s a minor thing in the grand scheme of what we’re doing,” Kaepernick said. “If we snap the ball with one second, that’s not a problem to us. Because we know we’re getting to something we like vs. their defense.”

Kaepernick got hit with two delay-of-game penalties in the Super Bowl XLVII loss to the Baltimore Ravens.

So what exactly goes on before that 40-second clock expires, during which time coach Jim Harbaugh relays in a play, Kaepernick relays it in the huddle and then analyzes the defense before their snap.

“It can vary on what we’re trying to get done that play, when the play call comes in, and if there’s multiple layers to the play,” Kaepernick said. “Is there something we need to check to? Did the defense show something that we need to change what we’re doing? All that has to happen within that 40 seconds.

“There are times when you get to the point you’re just running out of time to get to what you want to. And we have the feeling if we take the timeout to get something right and we end up getting points out of it, that’s a beneficial timeout for us, whether it’s early in the game, late in the game. Regardless, if we end up with points out of that timeout, we feel like that’s a good timeout used.”

On Tuesday, Harbaugh likened their timeout usage to a chess move, where he’s willing to sacrifice a pawn in order to capture an opponent’s queen.

Kaepernick said there are times where he must decide which play to audible into depending upon the defense’s different alignment.

“And it could be something based on what the defense is doing that week that we want to run this versus this look and this versus that look,” Kaepernick said. “The defense is always changing. So they might change, and then we have to change late. I think that’s where a lot of the time factor comes in for us.”

For more on the 49ers, see Cam Inman’s Hot Read blog at blogs.mercurynews.com/49ers. Follow him on Twitter at twitter.com/CamInman.