1. A method of operation of a navigation system comprising: extracting navigation-related web documents having a point of interest; generating formatting sequences of the navigation-related web documents; selecting a user-defined percentile representing reciprocal fraction of an expected number of clusters; calculating a threshold value for a first cluster with the threshold value to be equal to the user-defined percentile of a first normalized distribution of sample comparison values between the first cluster and formatting sequence samples from the formatting sequences, the first cluster is from the clusters; computing an associated comparison value between a first formatting sequence from the formatting sequences and the first cluster; grouping the first formatting sequence with the first cluster when the associated comparison value exceeds the threshold value for the first cluster; and generating a travel route for the point of interest related to the first cluster for displaying on a device.