Bacterial genome alignment with mauve

Question

[rthapa]

I am aligning query genome against reference genome of bacteria. I reordered the contigs in mauve but still the Linear collinear blocks (LCBs) are not in the same genome position of query genome compared to reference genome. Is there a way to re-order the contigs in such a way that LCBs are in same genome position in both? For e.g green LCBs should be in same position in both, and same with other LCBs.