The most methods for intrusion detection are based on the misuse detection which accumulates hewn intrusion information and makes a decision of an attack against any behavior data. However it is very difficult to detect a new or modified aoack with only the collected patterns of attack behaviors. Therefore, if considering that the method of anomaly behavior detection actually has a high false detection rate, a new approach is required for very huge intrusion patterns based on sequence. The approach can improve a possibility for intrusion detection of known attacks as well as modified and unknown attacks in addition to the similarity measurement of intrusion patterns. This paper proposes a method which applies the multiple sequence alignments technique to the similarity matching of the sequence based intrusion patterns. It enables the statistical analysis of sequence patterns and can be implemented easily. Also, the method reduces the number of detection alerts and false detection for attacks according to the changes of a sequence size.