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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. You can input the value as a sequence or name of the sequence in the FASTA format and sequence after that.

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     <img src="/wiki/download/attachments/4227320/Search in Sequence.png"/>
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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.

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