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. 2013 Nov 27;42(Database issue):D633–D642. doi: 10.1093/nar/gkt1244

Figure 2.

Figure 2.

Multiple sequence alignment of partial bacterial 16S rRNA sequences corresponding to the region between common V6 variable region amplification primers (15). Uppercase columns correspond to modeled positions. Lowercase columns correspond to regions where hypervariability in size and structure preclude assignment of homologous residues. These columns are normally ‘masked out’ before phylogenetic analysis. (A) Using the new RDP 11 alignment model. This matches the alignment for this region obtained with full-length sequences. (B) Using the RDP 10 alignment model. The alignment of the full-length sequences is almost identical in this V6 region between the two models, except one G-U pair in RDP 11 appears as inserts in the RDP 10 alignment. Bases highlighted in green color are canonical base pairs matching the conserved secondary structure. From top to bottom, the GenBank accessions are AB006164, AB006178, AB021164, AB015577, AB003932 and AB004715.