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After a little bit, a window will pop up showing the aligned genomes. It should look something like this
What's going on?
Form the Mauve manual:
"When a block lies above the center line the aligned region is in the forward orientation relative to the first genome sequence. Blocks below the center line indicate regions that align in the reverse complement (inverse) orientation. Regions outside blocks lack detectable homology among the input genomes. Inside each block Mauve draws a similarity profile of the genome sequence. The height of the similarity profile corresponds to the average level of conservation in that region of the genome sequence. Areas that are completely white were not aligned and probably contain sequence elements specific to a particular genome."
Navigating in Mauve
- You can move around and zoon zoom in and out using control and the arrow keys.
- You can click on a region in one genome to center the aligned regions in the other genome to it.
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