Dot-Plot comparison done using MUMmer of the DNA sequences of the R1- and r1-contig. Alignment between contigs starts at approximately 120 kbp in the R1-contig. The DNA sequence between approximately 120 kbp and 200 kbp of the R1-contig (B) was highly similar to the r1-contig and included a palindromic structure of around 34 kbp. The regions from 200 kbp to 245 kbp (C) and again from 375 to 400 kbp (F) of the R1-contig contained conserved repeated sequences that were interrupted and flanked by sequences with low similarity between the two contigs. Segment D from 245 to 330 kb showed no similarity to the r1-contig. The segment from 330 kbp to 400 kbp (E) of the R1-contig was inverted relative to the r1-contig.