Yes, you can specify trade lots...specification is done on unsettled trades...
in TD Ameritrade, during the window starting with the day after the trade until trade settlement day---you can go in and specify which lots you want settled on that trade...if you do nothing, the system will use whatever method is your default i.e. first in first out, etc...
don't know anything about Scottrade, but these instructions may help in your case: GL
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