Minecraft wiki entry for Thunderstorm, associated text: While the clear counter is counting down, the weather is always clear. This counter is used only when the "/weather clear" command is issued, setting the counter to a value given by the player or 5 minutes (see Commands/weather)
The rain counter counts down to zero, and each time it reaches zero, the rain is toggled on or off. When the rain is turned on, the counter is reset to a value between 12,000-23,999 ticks (0.5-1 game days), and when the rain is turned off the counter is reset to a value of 12,000-179,999 ticks (0.5-7.5 game days).
Like the rain counter, the thunder counter also toggles thunder on and off when it reaches zero, but clear weather overrides the "on" state. When thunder is turned on, the thunder counter is reset to 3,600-15,999 ticks (3-13 minutes), and when thunder is turned off the counter rests to 12,000-179,999 ticks (0.5-7.5 days).
Thunder can occur in the game only when the rain and thunder states both happen to be "on" at the same time. The random combinations of the states toggled by the rain and thunder counters result in a 1.44% chance for a thunderstorm to occur, or an approximate average real-time duration of 9 hours between thunderstorms.
The values in each range are uniformly distributed.