The jump countdown is written in Ancient, and is displayed down to the millisecond. It is measured in hours. When the time remaining drops below one minute, the timer emits a beeping sound followed by the numbers turning red. There are timers placed in every key area of the ship; the control interface room, the gate room and presumably many more, including external timers on the shuttles. If Destiny's FTL engine is disabled or disrupted by certain means, the countdown will not activate until the problem is corrected. (SGU: "Air, Part 2", "Divided", "Faith", "Sabotage", "Incursion, Part 2")
If a Stargate is active when the jump countdown reaches zero- and there is a reason to maintain the wormhole, such as an object having begun to enter the 'gate on the other end without having actually crossed through the event horizon-, the ship will not jump until the wormhole has been disconnected, although it will shake violently while the wormhole remains, suggesting that this method should not be used unless absolutely necessary (SGU: "Air, Part 3").
Destiny determines the jump countdown using a highly complex formula based on numerous variables, some of which tie into Destiny's actions after dropping out of FTL. For whatever reason, this formula does not seem to reflect the necessary amount of time to perform a task at a given location. When Rush "told" the ship of the current air supply and quality issues, Destiny dropped out of FTL, dialed a planet and set the time limit to a little over 12 hours despite the distance necessary to locate the needed supplies. Later, when it stopped at a Jungle planet, the countdown was set to around thirty-six hours despite the proximity of the necessary supplies to the gate. (SGU: "Air, Part 2", "Time", "Pathogen")
After unlocking the bridge, one of Rush's first acts was to attempt to understand the jump countdown and set it to his liking. However, his attempts to do this all ended in failure, causing the ship to drop out of FTL in areas with no Stargates and then randomly change course, confusing the crew. Rush filled a hallway with equations relating to the countdown, which he enlisted Chloe Armstrong's aid in solving. (SGU: "Aftermath", "Pathogen")