This is how you can do it:
volatile byte wantedPin; // which pin to pulse on and off
const byte PWMiterations = 40;
const byte PWMdutyCycle = 2; // <-- should be less than PWMiterations
volatile byte pwmCount;
ISR(TIMER1_COMPA_vect)
{
// if in "on" cycle turn the LED on
if (pwmCount > PWMdutyCycle)
digitalWrite(wantedPin, LOW);
else
digitalWrite(wantedPin, HIGH);
if (++pwmCount >= PWMiterations)
pwmCount = 0;
} // end of TIMER1_COMPA_vect
const int numberOfLEDs = 14;
const byte LEDorder [numberOfLEDs] = { 1, 2, 3, 4, 5, 7, 6, 8, 12, 9, 13, 10, 0, 11 };
void setup()
{
for (byte i = 0; i < numberOfLEDs; i++)
pinMode(LEDorder [i], OUTPUT);
// set up Timer 1
TCCR1A = 0; // normal operation
TCNT1 = 0; // make sure we start at zero
TCCR1B = _BV(WGM12) | _BV(CS10) | _BV (CS12); // CTC, scale to clock / 1024
OCR1A = 5; // compare A register value (1000 * clock speed / 1024)
TIMSK1 = _BV (OCIE1A); // interrupt on Compare A Match
} // end of setup
void doCircle (const unsigned long delayAmount)
{
for (byte i = 0; i < numberOfLEDs; i++)
{
noInterrupts ();
byte pin = LEDorder [i];
wantedPin = pin;
pwmCount = 0;
interrupts ();
delay(delayAmount);
digitalWrite(pin, LOW);
} // end of for
} // end of doCircle
void loop()
{
for (unsigned long n = 500; n > 0; n -= 100)
doCircle (n);
} // end of loop
Change the constant PWMdutyCycle to get it brighter or less bright. Right now it is fairly dull (2 / 40 cycles on, the rest off).