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  • Indexing - select the number to start counting from:
    • 1-based - the first column has number 0 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.