We demonstrate a means of detecting weak optical transitions in cold atoms that undergo cyclic (preparation, probing, and detection) routines with improved sensitivity. The gain in sensitivity is made by probing atoms on alternate cycles of a repeated experimental sequence, leading to regular modulation of the ground state atom population when at the resonance frequency. The atomic transition is identified by conducting a fast Fourier transform via an algorithm or instrument. We find an enhancement of detection sensitivity compared to more conventional scanning methods of ∼ 20 for the same sampling time, and can detect contemporary clock lines with fewer than 103 atoms in a magneto-optical trap. We apply the method to the (6 s 2) 1 S 0 - (6 s 6 p) 3 P 0 clock transition in 171Yb and 173Yb. In addition, the ac-Stark shift of this line in 171Yb is measured to be 0.19(3) kHz W - 1 m2 at 556 nm.