STM32F4 Discovery Board timers, PWM and LEDs
this is the default clock tree of STM32F4 discovery board, initialized with STM32CubeMX (with or without choosing default peripherals settings). the default clock for timers is 12.5 MHz (depending on which bus timer is connected to, refer to datasheet, in you case, both are connected to APB1).



also, using interrupts for TIM4 to drive the LED is not a good practice. you should use PWM generation CH4 in CubeMX as the blue LED is connected to PD15, which is CH4 of TIM4 itself. (the PD15 ouput is used for another purpose in the board at startup settings, you have to click on the pin in the image in CubeMX choose reset state. then you can choose PWM generation CH4 in the TIM4 settings.