We demonstrate a means of detecting weak optical transitions in cold atoms that undergo cyclic routines with high sensitivity. The gain in sensitivity is made by probing atoms on alternate cycles leading to a 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 algorithm or instrument. We find an enhancement of detection sensitivity compared to more conventional scanning methods of $sim 20$ for the same sampling time, and can detect clock lines with fewer than $10^3$ atoms in a magneto-optical trap. We apply the method to the $(6s^{2})$ $ ^{1}S_{0} - (6s6p)$ $^{3}P_{0}$ clock transition in $^{171}$Yb and $^{173}$Yb. The ac-Stark shift of this line in $^{171}$Yb is measured to be 0.19(3) kHz$cdot$W$^{-1}cdot$m$^2$ at 556 nm.
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