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In the Save annotation(s) to group you can set up a file to store annotations.  It could be either an existing annotation table object or a new annotation table.

In the Annotation parameters group you can specify the name of the group and the name of the annotation. If the group name is set to <auto> UGENE will use the group name as the name for the group. You can use the ‘/’ characters in this field as a group name separator to create subgroups. If the annotation name is set to by type UGENE will use the annotation type from the Annotation type: table as the name for the annotation. Also you can add a description in the corresponding text field. To use a pattern name for the annotations check the corresponding checkbox.

After that click the Create annotations button. The annotations will be created. Also you can see the result statistic and navigation under the Search for: field:

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Searching for one or several patterns and names of the result annotations

If you search for one pattern only, than input the required name into the Annotation name field and leave the Use pattern name check box unchecked.

You can also search for several patterns at a time by:

• Inputting several patterns into the search field (click <Ctrl> + <Enter> keys to insert to a new line):
  

• Inputting several patterns into the search filed in FASTA format:
  
• Loading patterns from a FASTA file

Even when you search for several patterns, names of the found annotations will be identical by default (the name is specified in the Annotation name field).

If you want to assign different names to annotations found for different patterns, than you should:

• Input the patterns in FASTA format (the latter two cases above)
• Check the Use pattern name checkbox in the Annotation parameters group

Here is an example of the found annotations in the Annotations Editor: