Figure

Width of figure: The width of the image generated in pixels.

Thickness of genome line: Thickness in pixels of the line representing the full sequence.

Height of genes in figure: The height of the annotation parts of the figure.

Height of blast hits in figure: The height of the regions showing blast matches. The total height of the figure generated will be (no of annotation files x height of genes in figure) + (no of blast files x height of blast hits in figure).

Alignment of genomes: Left, right, centre, best blast. Genomes can be aligned on the left, the right or centered in the middle of the figure. Alternatively they can be aligned so that each genome is perpendicular to the adjacent genomes at the site of their best blast hit.

Draw blast identity legend: Draws a colour gradient legend for visualising the identity of your blast hits.

Scale legend: Draws a H bracket of the size specified in base pairs for help visualising the length of your genomes. The default “0� will mean there is no scale legend drawn.

Feature Legend: Creates legend of all the features used in the image.

Get feature names from: Gets feature names from this descriptor in the genbank/embl file