Output of different cut-offs for the Link Threshold (LT) and Merge Threshold (MT) when comparing H. pylori R056A and H. pylori P12. Different user-defined cut-offs affect the output display of the two aligned genomes. The top three plots were generated at genome identity of 95% and MT of 0 bp, but at different LT cut-offs. The three plots at the bottom were generated at genome identity of 95% and LT of 1,000 bp, but at different MT cut-offs. Each half circle (either left or right) represents each separate genome/assembly. The coloured links show the homologous regions in the two selected genomes. The green track is the alignment histogram; each 10 Kbp window in the diagram is represented by a histogram bar and 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 non-specific alignment or windows containing repetitive regions. A trough may indicate an unmapped region which could be an insertion e.g. prophage insertion. We can clearly observe how different user-defined thresholds affect the display of the two aligned genomes.