To search for a pattern(s) in alignment go to the Search in Alignment tab of the Options Panel.
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The following parameters are available:
This group specifies the search context that should be used to search for a pattern. It is possible to search patterns in sequences or in sequence names.
To search for a pattern(s) input the value you want to search in the text field.
Press the Next button to search in the direction “From left to right, from top to bottom”. Press the Previous button 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.
To group results press Group button. The results will be selected and grouped to the top after the first click or to the bottom after the second click to the button.
This group specifies the algorithm that should be used to search for a pattern. The algorithm can be one of the following:
In this group, you can specify the sequence range where to search for a pattern. You can search in the whole alignment, specify a custom region or search in the selected region.
This group contains additional common settings:
Remove overlapped results — annotates only one of the overlapped results.
Limit results number to — limits the number of the searched results to the specified value.