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To search for a pattern(s) in alignment go to the Search in Alignment tab of the Options Panel.

Input the value you want to search in the text field and click the Search button. 

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By default, misc_feature annotations are created for regions that exactly match the pattern. Find below the description of the available settings.

Children Display
all true

You can search for a pattern inside an alignment.

Enter a query string in the edit box under the Sequence area.

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Press the right arrow to search in the direction “From left to right, from top to bottom”. Press the left arrow to search in the direction “From right to left, from bottom to top”. If the pattern is found, the result will be focused and highlighted in the Sequence area. You can continue the search in any direction from this position.