With the advent of cloud computing, secure outsourcing techniques of sequence comparisons are becoming increasingly valuable, especially for clients with limited resources. One of the most critical functionalities in data outsourcing is verifiability. However, there is very few secure outsourcing scheme for sequence comparisons that the clients can verify whether the servers honestly execute a protocol or not. In this paper, we tackle the problem by integrating the technique of garbled circuit with homomorphic encryption. As compared to existing schemes, our proposed solution enables clients to efficiently detect the dishonesty of servers. In particular, our construction re-garbles the circuit only for malformed responses and hence is very efficient. Besides, we also present the formal analysis for our proposed construction.