Use the analog pin to read voltage levels, maybe the voltage on a potentiometer for example, then do something with the resulting 0-1023 result (representing 4.89mV steps).
A0-A5 can be used as analog inputs, or as digital input/outputs.
I don't think D13 flashes during programming, I think at the most it just turns off after the download starts.
If you have an FTDI-Basic or equivalent
for programming, it has LEDs that flash during programming.
These are the 2 yellow LEDs in the bottom middle of the UNO schematic.