The problem of aligning motifs in variable regions: The HIV envelope protein (ENV) sequence [5].

The bottom strip shows an overview of the first half of the alignment. At the top, one of the variable (V1, left) and constant (C3, right) regions are shown. N-linked glycosylation is crucial for the immune evasion function of ENV; hence there is a prevalence of the N-{P}-[ST]-{P} motifs throughout. In C3 (right), the motifs are clearly well-aligned; however in the variable V1 (left), even though conserved flanking regions give a convenient anchoring for the alignment, it is obvious that the motifs are poorly aligned. This alignment was created with Clustal Omega [6]. For clarity, only a subset of representative sequences (one per patient) is shown here. Figures were created using Jalview [18]; the presence of N-terminal glycosylation motifs is shown in yellow.