Global alignment of P. polymyxa plasmids pM1 and pSC2. The local collinear block (LCB) plot was generated using the progressiveMauve algorithm using default parameters. The plasmid visualized is listed below each respective LCB plot. Global alignments are visualized as LCBs, which represent regions of chromosomal similarity between strains. Five very short and dispersed LCBs were identified between the two plasmids and regions with the same colour represent homologous LCBs in the other plasmid. Regions without colour both within and between local collinear blocks represent presence of strain-specific sequence. Local collinear blocks drawn below the horizontal correspond to inversions. Comparison of pM1 and pSC2 versus their own respective genomes and the genomes of other strains yielded no LCBs and is thus omitted.