One embodiment of the present invention relates to a digital phase locked loop (ADPLL) configured to generate a plurality of time-aligned output clock signals having different frequency values. The ADPLL comprises a digital controlled oscillator configured to generate a variable clock signal that is separated into two signal paths operating according to two separate clock domains. A first signal path is configured to generate a feedback signal that synchronizes the variable clock signal with a reference signal. A second signal path comprises a clock divider circuit configured to synchronously divide the variable clock signal to automatically generate a plurality of time-aligned output clock signals having different frequencies. A clock aligner monitors a phase difference between the variable clock signal and one of the plurality of time-aligned output clock signals and generates a control signal that causes a programmable delay line to automatically time-align the output clock signals with the variable clock signal.