Ok here (Resource\Themes\Civ4\Civ4Theme_Common.thm) are the changes
GColor .EndTurnDot_Green = GColor(155,176,121,255);
GColor .EndTurnDot_Red = GColor(181, 60, 60,255);
GColor .EndTurnDot_DarkRed = GColor(100, 30, 30,255);
GColor .EndTurnDot_Disable = GColor(128,128,128,255);
The numbers in brackets are GColor(Red,Green,Blue,Alpha)