On the 2001 Honda Civic, the intake valves should be set within the tolerances of .007"-.009" and the exhaust valve clearance should be set within the tolerances of .009"-.011". First you set the engine to top dead center by rotating the crankshaft pulley so the white marker dot is lined up with the timing mark on the engine. Now look for the camshaft pulley where it has the word "up" written on it. The word "up" should be in the straight up position when checking the number 1 piston's valve clearances. Then rotate the crankshaft 180 degrees and the camshaft will turn 90 degrees. The "up" will be facing the 9 o'clock piston and you can then check the number 3 piston's valve clearances. Rotate the crankshaft another 180 degrees and the camshaft will turn 90 degrees again. You can now check the number 4 piston's valve clearances. Rotate the crankshaft one more time 180 degrees and the camshaft will turn 90 degrees again. You can now make the final adjustments on the number 2 piston's valve clearances.
The piston sequence runs 1-2-3-4 from the driver side (where the belts are) toward the passenger side.