Alu Sequence alignment. The consensus sequence for the ancestral Alu Y subfamily is shown at the top. The dots represent the same nucleotide as Alu Y. Deletions are shown as dashes and mutations are shown as the corrected base. The chromosome 7 locus has a number of mutations different from Alu Y that are shared by all investigated species (highlighted in gray) and are all located in the right monomer of the element following the middle A-rich region. Post-insertion, the chromosome 7 locus in the orangutan (labeled Orangutan Chr7) independently acquired sequential diagnostic mutations (highlighted in yellow) shared by all polymorphic loci of the young Alu Ye5b5_Pongo subfamily in orangutans (starting with O:Chr). At some point, one of the Alu Ye5b5_Pongo members subsequently acquired one substitution and one deletion (highlighted in aqua) and has propagated as a daughter subfamily. Following the divergence of orangutan and the lineage leading to humans, the chromosome 7 locus acquired three substitutions (highlighted in green) shared in gorilla, chimpanzee and human. There is one human-specific Alu insertion, H: Chr3, which shares these three variants.