To copy the current selection click the Copy/Paste ‣ Copy selection item in the Actions main menu or the context menu. The hotkey for this action is Ctrl-C.

Also, you can copy the selection in different formats, for example, FASTA, CLUSTALW, RICH TEXT(HTML), NEXUS, MSF.

To copy subalignment in selected format do the following:

To paste any of copied selections use the Copy/Paste->Paste context menu item or Ctrl+V shortcut.

To paste content before selection use the Copy/Paste->Paste (before selection) context menu item or Ctrl+Alt+V shortcut.

To cut the selection use the Copy/Paste->Cut context menu item or Ctrl+X  shortcut.

To copy the whole row(s) use the corresponding context menu item.