Clock control sequence reconstruction is an important phase in the cryptanalysis of irregularly clocked Linear Feedback Shift Registers(LFSRs). The methods of reconstruction proposed so far have been designed to work in the known plaintext attack scenario, i.e. without noise. We present a clock control reconstruction procedure intended to function in the ciphertext only attack scenario. The reconstruction is performed by a directed depth-first like search through the edit distance matrix. The directedness of the search is achieved by gradually increasing the permitted weight deviation from the optimal one, and by limiting it according to the noise level in the statistical model of the generator. The experimental results show that the total number of candidate clock control sequences increases moderately as the probability of noise and/or the necessary clock control sequence length increase. The attack is effective even if the noise level is relatively high and the solution is guaranteed to be found.