Fig. 3

Pairwise genome comparison between the L. monocytogenes SLCC2376 and L. monocytogenes HCC23 from the lineage III. Three noticeable gaps and insertions can be observed and labelled as 1, 2 and 3 in circles found in the genome sequences of HCC23 and SLCC2376, which predicted to be putative prophage regions by PHAST. Two are intact prophages, whereas another one is a questionable (close to complete) prophage. The green track indicates the histogram bars. Each 10 Kbp window in the diagram is assigned by a histogram bar. The height of each bar illustrates the total number of bases of the opposite genome aligned to this 10 Kbp window region. The upper border of the grey area delineates 10 Kbp height. If the height is higher than the 10 Kbp, it may indicate the genomic region is not specific or containing repetitive regions. A gap may indicate unmapped region which could be an insertion e.g. prophages