A method of identifying similar media items is described. The method include identifying a first multiplicity of fingerprints representative of content segments of variable duration for a first media item and a second multiplicity of fingerprints representative of content segments of variable duration for a second media item. The method further includes comparing, by a processing device, a first group of the first multiplicity of fingerprints to a second group of the second multiplicity of fingerprints to generate a first similarity score indicative of a similarity between the first group of fingerprints and the second group of fingerprints. The method also includes determining an alignment score for the first multiplicity of fingerprints and the second multiplicity of fingerprints using the first similarity score.