an A would be represented by two dashes
That would be M. A would be dot-dash.
You will need to describe the electronics and its outputs much more clearly. This does not make sense:
a positive peak(max) represents left eye movement and the minimum peak represents right eye movement.
The Arduino ADC can read only positive voltages, 0-5V on a standard Uno.
Obviously, timing is very important. Use the millis() function to keep track.