I didn't mark my wires when I put in new in Honeywell CT78N thermostat. It worked until I tried my air conditioner and the pump won't come on. I think the wires are crossed,what color go where?

What colors do you have at the stat, and what letters are on the stat? I will also need to know what colored wires hook to what letters in the furnace.

Standard is red to r, white to w, green to g, yellow (maybe blue) to y, and maybe blue or black to c. This may change if you have a heat pump system.