Repetitive sequence analysis. a. Distribution of the putative hrs in the EpapGV genome with their respective palindromes. b. Predicted secondary structure of the two largest palindromes. The central palindrome used in the multiple alignment is boxed with a dashed line. c. Structure of the putative non-hr ori. d. Alignment of all the palindromes excluding hr4b. Genome positions are indicated at both ends of the aligned sequences. Conserved 15 bp ends are boxed. e. Sequence logo performed with the multiple alignment of the palindromes. f. Comparison between consensus EpapGV palindromic ends with the consensus 13 bp ends reported by Hilton & Winstanley (2008)  (see Figure 3 of this reference).
Ferrelli et al. BMC Genomics 2012 13:548 doi:10.1186/1471-2164-13-548