Figure 1

Core alignment and associated phylogeny of 1416 Lm SIDER sequences. All previously annotated Lm SIDER sequences encompassing 350–700 nt were extracted and submitted to HMM profile training using the simulated annealing and Baum-Welch expectation maximization algorithms implemented in HMMER-1.8.5 [65]. Columns containing more than 75% gap characters and failing to present a 10% consensus residue were removed to ease representation. The associated minimal evolution phylogeny, which was scaled to the alignment overview, was inferred with MEGA4 [66] based on p-distance and considering pairwise deletions. The red and blue clusters correspond to SIDER2 and SIDER1 sequences, respectively, whereas the grey cluster contains equal proportions of both SIDERs. Nucleotide composition is as follows: green = adenine; red = thymine; blue = cytosine; orange = guanine. The individual phylogeny and full alignment can be viewed in Additional file 1.