IDENTIFYING REPEAT SUBSEQUENCES BY LEFT AND RIGHT CONTEXTS

A system and method of identifying repeat subsequences having at least a value of x for threshold of different left contexts and a value of y for a threshold of different right contexts for an input sequence are disclosed. The method may include generating a lexicographically sorted suffix array for the input sequence and a longest common prefix array. The suffix array is traversed in lexicographic order comparing the longest common prefix values between consecutive suffixes. Suffixes with the same longest common prefix are representative of occurrence of the same repeat, a higher longest common prefix indicates a new occurrence of a longer repeat, and a lower longest common prefix indicates the last occurrence of a repeat.