|Increase/decrease the amount of vertical space between sequence blocks||Use the Spacing slider. This command does not affect the sizes of the alignment blocks, but only the amount of white space between them. To make the alignment blocks increase/decrease in size, instead use the Overview’s zoom in/out.|
|Change font options for the ruler numbers in the Overview||Use the Font drop-down menu to choose a font for the ruler numbers in the Overview. Recently selected fonts (if any) appear at the top of the menu, and other available fonts appear below the row of dashes. Enter the preferred font size by typing a number between 4-72 in the box at right, or by using the corresponding up and down arrows ( ). See note below for additional clarification.|
|Select font options for other items in the Overview|| To set a different font for sequence and track labels, first check the box next to Track names font. If desired, use the corresponding drop-down menu to change the font from the current value. Enter the preferred font size by typing a number between 4-72 in the box at right, or by using the corresponding up and down arrows ( ).
p(banner tip). Note: When Track names font is unchecked and tracks are open, Font and Font size (described above) affect everything in the view. When Track names font is checked and tracks are open, Font and Font size affect only the rulers, while Track names font and Track names font size affect sequence labels and track labels.
|Display or hide the lines connecting blocks from one track to another||Check or uncheck the Show connecting lines checkbox. This option is only enabled for multi-block (Mauve) alignments.|
|Specify the reference sequence||To use one of the aligned sequences as the reference, make a selection from the Reference drop-down menu. This option is only enabled for multi-block (Mauve) alignments, and changes the lines that connect the blocks. All blocks for the selected reference will be placed on the forward strand. Blocks for non-reference sequences can appear on either strand.|
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