FIG 1.

Global DNA alignment of the WT FMDV infectious clone (pRMC35) P1 region and the deoptimized infectious clone (pA12-P1Deopt). WT and deoptimized sequences were aligned using Clone Manager Suite V8 (Scientific & Educational Software, Morrisville, NC). The alignment includes P1 and 5′/3′ flanking regions with PflMI restriction sites (used for swapping the capsid coding region). All structural proteins within the P1 region (VP4, VP2, VP3, and VP1) are indicated, as well as nonstructural protein 2A and fragments of the 2B and L proteins.