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To align a sequence to the an opened alignment, click the Align sequence to this alignment toolbar button:

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     <img src="/wiki/download/attachments/16126085/Aligning Sequence to this Alignment.png"/>
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Choose a file with the sequence from the files system, and click Open buttonOpen.

Also, you can select add an already opened in project view sequence and sequence or sequences to the alignment. To do it, select the sequence object(s) in the Project View and click the Align sequence to this alignment toolbar button. In this case the sequence The sequence(s) will be aligned to the alignment automatically.