Table 5.

Examples for dealing with SSE variability in a block. Ambiguous regions are highlighted in bold and italics:

SSEs in some blocks	Given consensus	Explanation
HLLSSLLLL HLLLLLLLL HLLHSLLLL	HL	Identical flanks, ambiguous region contains flank SSE.
HLLLLTLLL HLLLLTLLL HLLTTTLLL	HLTL	Different flanks, ambiguous region contains only flank SSEs.
HLLLLTLLL HLLLSTLLL HLLTTTLLL	No consensus	Different flanks, strand is not one of the flank SSEs.
HLLSSSLLLL HLLLLLLLLL HLLHSSLLLL	No consensus	Three consecutive ambiguous positions.
HLLTSTLLLL HLLTHTLLLL HLLTLTLLLL	No consensus	Identical flanks, ambiguous region does not contain flank SSE.