Select the output file to export the highlighting, choose exported area and click on the Export button. The task report will appear in the Notifications.

Also, you may set additional parameters:

• Indexing - select the number to start counting from:
  • 1-based - the first column has number 1,
  • 0-based - the first column has number 0.
• Keep gaps - check if you want to store gap symbols in the result file.
• Dots instead not highlighted - replace not-highlighted bases with dots in the result file.
• Transpose output - if this checkbox is checked, the sequences will be located horizontally (not vertically, as in UGENE). May be useful, if you have a long alignment, but not many sequences.