To copy 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 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 selection use the Copy/Paste->Paste context menu item or Ctrl+V shortcut.