Fig. 2

High similarity between R1S1 and ACAM34 primary replicons. a NUCmer plot [29] of R1S1 and ACAM34 primary replicons. The black circle highlights the Hlac-Pro1 provirus that is absent in R1S1. b Synteny between R1S1 and ACAM34 primary replicons. The red area connects sequences of the ACAM34 (upper horizontal bar) and R1S1 (lower horizontal bar) primary replicon that share high nucleotide identity: identity was > 99% with the exception of five regions with < 99% identity (blue bars; see Additional file 2: Table S6). Unique genes are highlighted as annotated black bars (Additional file 2: Table S4). In order to commence the alignment at the same sequence for both replicons, 80 ‘Ns’ were added to the end of the R1S1 replicon (to represent the unsequenced nucleotides) and the first 289,989 nucleotides were relocated to the end of the replicon