The game play clock is 40 seconds, not 25.
You are correct, the default is 40 seconds, however it can be, and often is, set to 25 seconds. The key is "at the end of the play" as to when it starts. That includes "taking a knee".
Below are the details AND WHEN it gets
adjusted to 25 seconds to start play. The below does not discuss the 10 second "run off" that is an option toward the end of each half.
The 40/25 Second Clock Operator will be instructed to:
1) Set the clock display to
25 seconds before the game and second half starts (first play is a kickoff).
2) For kickoff, start the
25-second clock when signaled to do so by the Referee.
3) The play clock will automatically reset to 40 seconds
at the end of each play.
4) The covering official’s signal will designate when to start the play clock.
5) Start 40-second clock when the official signals:
a) The ball is dead in field of play: Play clock starts when covering official raises his arm or gives a wind signal if near the sideline.
b) Incomplete pass: Play clock starts when covering official signals incomplete pass.
c) Ball dead out of bounds: Play clock starts when covering official signals to stop the game clock.
6)
Manually set the play clock to 25 seconds when any official signals to stop the game clock for: a penalty, a charged team timeout, media or injury timeout, measurement, change of possession, after any kick down, any score, first play of a quarter, or first play of a team’s series in overtime. Then start the play clock when the Referee next gives the wind the clock or ready for play signal.
7) The play clock will also be set to
25 seconds if signal to do so by the Referee (one hand pump above the head or the Referee’s ready for play signal). Under no circumstances should the play clock be reset to
25 seconds upon a signal by any official other than the referee. It is common practice for officials to communicate to the referee to "ask" if he wants to consider resetting by making the pumping signal. Resetting is the sole discretion of the referee.
8) Leave display at '00' seconds if there is a delay of game penalty called until the Referee has completed his signals to the press box after enforcing the delay of game penalty. After a delay of game penalty has been enforced, set play clock to
25 seconds.
9) If the 40-second count is interrupted or stopped due to a play clock problem, the referee shall stop the game clock and then give a signal (both palms open in an over-the-head pumping motion). This means that the play clock should be re-set to 40 seconds and started immediately.
10) If the 40-second clock is running and the ball is not ready to be snapped after 20 seconds into the count (it might be at 25 seconds now dependent upon league...), the referee shall call timeout and signal that the play clock be set to
25 seconds. When play is to be resumed, the referee will give the ready-for-play signal and the play clock will begin the
25-second count.