An indexing system uses a graph-like data structure that clusters features indexes together. The minimum atomic value in the data structure is represented as a leaf node which is either a single feature index or a sequence of two or more feature indexes when a minimum sequence length is imposed. Root nodes are formed as clustered collections of leaf nodes and/or other root nodes. Context nodes are formed from root nodes that are associated with content that is being indexed. Links between a root node and other nodes each include a sequence order value that is used to maintain the sequencing order for feature indexes relative to the root node. The collection of nodes forms a graph-like data structure, where each context node is indexed according to the sequenced pattern of feature indexes. Clusters can be split, merged, and promoted to increase the efficiency in searching the data structure.