BMC Genomics 2009, 10:101 Additional material Additional file 1 Results of RNAz analysis of Sequence #1. The top table summarizes the sequence input and RNA structure properties. The middle diagram shows the base pairs formed between five of the repeat sequences as well as the consensus sequence. The predicted RNA secondary structure is shown at the bottom. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S1.doc] Additional file 2 Alignment of nucleotide sequences from eleven plasmid sequences related to B. afzelii PKo lp34 Sequence #2. The alignment shows invar- iant positions as well base substitutions and deletions. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S2.doc] Additional file 3 RNA secondary structure models of Sequence #2-related nucleotide sequences from different plasmids. Stem loop structures are highly con- served between sequences displaying base substitutions and deletions. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S3.jpeg] Additional file 4 Amino acid sequence alignment of CRASP-1 (Ba_lp54_mmsa_71_experimentally determined) and related loci BAPKO_2065-2070. The alignment shows conserved and modified amino acid positions. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S4.doc] Additional file 5 RNA secondary structure models of Sequence #3 nt sequences. Second- ary structure models show two conserved stem loops. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S5.doc] Additional file 6 Alignment of Sequence #4 and related nucleotide sequences. Align- ment shows major changes in nucleotide sequences from positions 53– 122. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S6.doc] Additional file 7 RNA secondary structure models of Sequence #4 and related sequences. Conservation of overall secondary structure is maintained in the presence of major changes in nucleotide sequence. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S7.doc] http://www.biomedcentral.com/1471-2164/10/101 Additional file 8 RNA secondary structure model of Sequence #5 from plasmid Bb lp54. Three stem loops are depicted that are conserved in related sequences. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S8.doc] Additional file 9 RNAz analysis of Sequence #5. Conserved RNA secondary structure parameters are shown. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-101-S9.doc] Acknowledgements I thank Dr. Jorge Benach for original suggestions of analyzing Borrelia plas- mids for RNA sequences and for constructive comments on the manu- script. Work supported in part by Department of Molecular Genetic and Microbiology, SUNY, Stony Brook. References 1. 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