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GT W853 Alignment Viewer Tab Pane

In the Align View tab pane, you can change the display settings of Alignment Viewer.

  • Scroll and zoom setting of Feature Pane
  • Automatic scroll setting of Fragment Pane
  • Display limit setting
  • Pane display order setting

Map Scale Parameters section:

In this section, you set the zoom and side scroll of the main feature map.

Zoom In pull-down menu: Select the zoom magnification of the feature map from the pull-down menu. With one mouse click, X2 will be doubled, X4 will be 4 times and X8 will be 8 times enlarged.

Zoom Out pull-down menu: Select magnification of the zoom out of the feature map from the pull-down menu. With one mouse click, X2 will be reduced by 2 times, X4 by 4 times, X8 by 8 times.

Base Shift Left pull-down menu: Select the left scroll width of Sequence Lane from the pull-down menu. Select the left scroll width when the horizontal size of Sequence Lane is set to 1. With one mouse click, 1 scrolls the same width, ½ scrolls the width of 1/2 and 1/4 scrolls a quarter width.

Base Shigt Right pull-down menu: Select the left scroll width of Sequence Lane from the pull-down menu. Select the right scroll width when the horizontal size of Sequence Lane is set to 1. With one mouse click, 1 scrolls the same width, 1/2 is half width, 1/4 is right quarter width.

Map Shift Left pull-down menu: Select the horizontal scroll width of the main feature map from the pull-down menu. Select the left scroll width when the horizontal feature size of the main feature map is 1. With one mouse click, 1 scrolls the same width, ½ scrolls the width of 1/2 and 1/4 scrolls a quarter width.

Map Shift Right pull-down menu: Select the horizontal scroll width of the main feature map from the pull-down menu. Select the right scroll width when the horizontal feature size of the main feature map is 1. With one mouse click, 1 scrolls the same width, 1/2 is half width, 1/4 is right quarter width.

Auto Scroll section:

Type radio button: Specify how to display the Read sequence in Consensus (Sequence Alignment) Pane.

North West Radio Button: When on, when scrolling horizontally, the top Read in the sequence display area is displayed in the upper left corner.

Center Radio Button: When on, scroll horizontally to display the center Read in the sequence display area.

South East Radio Button: When on, when scrolling horizontally, the bottom Read in the sequence display area is displayed in the bottom right corner.

Limitation section

Allocate Contig Range (bp) Input field: Enter a positive integer. When mapping to the reference genome, the reference genome is divided with this size, and IO occurs every time contig moves by horizotal scrolling operation. Increasing this size will allow faster display but a larger memory is required.

When [Packing Arrangement] Policy is selected, set the maximum depth to display input field: Enter an integer greater than or equal to zero. If it is zero, it is unlimited. Up to the Depth of the entered numerical value is displayed, and when it exceeds it, only the Read up to the specified Depth is displayed.

Allocate Memory for Mapped Read Sequences checkbox: If checked, reserves the mapped memory for Read.

Draw Area (Pane) Order Section

Set the display order of the four panes. Mouse drag and drop to change the order.

  • Navigation Area: Display Navigation Pane
  • Feature Area: Display of Feature Pane
  • Sequence Area: Display of Consensus Pane
  • Fragment Area: Display of Fragment Pane

"Set" button: Applies the changed parameters.

"Cancel" button: Cancel without applying the changed parameters.

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