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RNA secondary structure models of Sequence #1 nt sequences from a) Bb lp17 b) Ba lp25 and c) Bb lp28-4. The mfold (version 3.2) program by Zuker and Turner [28,29] was used for secondary structure modeling. Figure 2c shows base substitutions (marked with red arrows) that are found in all positions in the nine plasmid sequences.
