Fig. 1
From: Insertion and deletion polymorphisms of the ancient AluS family in the human genome
Diagnostic nucleotides differentiate AluS and AluY elements. a Five diagnostic nucleotides that distinguish RepBase consensus sequences of all six AluS subfamilies (AluSc, AluSg, AluSp, AluSq, AluSx, AluSz,) from the most common AluY subfamilies (AluY, AluYa5, AluYa8, AluYb8, AluYb9, AluYc1) were identified [3]. b Five diagnostic positions indicated in part (a) in the context of Alu sequence confirms AluS subfamily classification. The seven AluS TPRT insertion candidates are shown. AluS specific nucleotides at the diagnostic positions are highlighted in green, AluY specific nucleotides at the diagnostic positions are highlighted in red, and nucleotides at the diagnostic positions that are neither AluS nor AluY specific are highlighted in yellow. Further analysis of the polymorphic Alu element at 11q14.1, which has features of both AluS and AluY elements, that led to its ultimate classification as an AluS element is shown in Additional file 2: Figure S1