BMC Genomics 2009, 10:101 http://www.biomedcentral.com/1471-2164/10/101 Table 1: Nucleotide sequences that display secondary structure features Species SEQUENCE #1 B. afzelii PKo SEQUENCE #2 B. afzelii PKo SEQUENCE #3 B. afzelii PKo SEQUENCE #4 B. afzelii PKo SEQUENCE #5 B. burgdorferi B31 Plasmid lp25 lp34 lp60 lp60 lp54 Positions 573–632 1711–1804 50661–50585 26239–26360 14820–14969 Sequence ATAACAAAGAATTCTCCACC TATAATTTCTATGAAATTTAG GTGGAGATGAATTTGTTAA TAAAAGCATATCTTTTA TTAAAGATATGCTTAAT ATACTAAATAAACAAAAAATT AATACGTTGCACTTTATATTT TTTAAAAAAGAGAAGTTAATT CTTCTCTTTTTTTT ATTGGGTTTAAAACTACA AATAGGGCCTTAAGGCC CTATTTGTAGTTTTAAAGA AGTTTTCAATGAATTGTTA ATTTATAACAATAAACAAGT ATATATCTCACTATAGTTT TTTTCAAATA AATATTTATTTGCAAAACTT GAAAAGTTAGTGTATACTTT ATAGGTACAGACTGACACGC AATGTGTCGCTCTTAATATAA GGACCTGTTACCTTAAAGGGT TTATTGGGGATTCTTTTAAAA GAATCCCCAATAAACCCTTTA ACTTTT functional unit that may not show prominent conserved secondary structure motifs. Sequence #1 was also analyzed by the RNAz bioinformat- ics program [30], which predicts RNA structures that may be evolutionarily conserved. The results as depicted on the RNAz website are shown in Additional file 1. The second- ary structure displayed at the bottom of Additional file 1 is identical to that depicted in Figure 2c. The descriptive section at the top of the figure reveals a mean z-score of - 6.43 (a score less than 0.0 indicates that a structure is more stable than one expected by chance). The prediction is that Sequences #1 represents evolutionarily conserved RNA structures. Base pairing for five individual sequences is shown in the middle section of Additional file 1. Thus the RNAz analysis confirms the predicted evolutionary conservation of Sequence #1 secondary structures derived manually. In terms of nearest neighbor genes, the 60 nt repeat ele- ment is not located upstream or downstream of plasmid annotated genes in a consistent manner, both in terms of spacing and type of gene, although it is close to two puta- tive transposase genes. For example, the repeat element is found 39 bp upstream of locus BAPKO_4522 in Ba lp28. This locus encodes a putative 378 aa transposase. In Bb lp28-4, it is situated 37 base pairs downstream of locus BB_I41, which encodes a putative 80 aa protein. BB_I41 is a fragmented gene and shares the 5' end of a 155 aa trans- posase encoded by BB_H40 in Bb lp28-3. In Bb lp28-2, the 60 base pair repeat sequence overlaps the 3' end of BB_G01 by 3 bp. Locus BB_G01 encodes a 297 aa hypo- thetical protein. Sequence #2 A second set of repeat sequences displays inverted repeats and these are found in eleven loci in ten plasmids from the three Borrelia species, B. burgdorferi, B. afzelii and B. garinii. Alignment of nt sequences reveals there are a sig- nificant number of base substitutions as well as inser- tions/and or deletions [see Additional file 2]. Nucleotide positions 4–31 (sequence numbering positions from Ba lp34) comprise inverted repeats. RNA secondary structure modeling of putative RNA tran- scripts shows that all eleven sequences display stem loop Page 3 of 12 (page number not for citation purposes)