boolean toggle = 0; // boolean for the 5 second process

void setup() {
  // put your setup code here, to run once:
  pinMode(13, OUTPUT); // pin with led connected

  cli();//stop interrupts

  TCCR0A = 0;// set entire TCCR2A register to 0
  TCCR0B = 0;// same for TCCR2B
  TCNT0  = 0;//initialize counter value to 0
  // set compare match register for 2khz increments
  OCR0A = 255;// = (16*10^6) / (2000*64) - 1 (must be <256)
  // turn on CTC mode
  TCCR0A |= (1 << WGM01);
  // Set CS01 and CS00 bits for 64 prescaler
  TCCR0B |= (1 << CS01) | (1 << CS00);   
  // enable timer compare interrupt
  TIMSK0 |= (1 << OCIE0A);


  TCCR1A = 0;// set entire TCCR1A register to 0
  TCCR1B = 0;// same for TCCR1B
  TCNT1  = 0;//initialize counter value to 0
  // set compare match register for 1hz increments
  OCR1A = 39000;// = (16*10^6) / (1*1024) - 1 (must be <65536)
  // above set to value for approx 2.5 sec interval
  // turn on CTC mode
  TCCR1B |= (1 << WGM12);
  // Set CS12 and CS10 bits for 1024 prescaler
  TCCR1B |= (1 << CS12) | (1 << CS10);  
  // enable timer compare interrupt
  TIMSK1 |= (1 << OCIE1A);

  sei();//allow interrupts
}

ISR(TIMER0_COMPA_vect){// isr for light on
 digitalWrite(13,LOW); // turns led off after time 
}

ISR(TIMER1_COMPA_vect){// isr for light off
//(takes two cycles for full wave- toggle high then toggle low)
  if (toggle == 0){
    toggle = 1; //first 2.5 sec to pass does nothing
  } else if (toggle == 1){ // on second 2.5 second to pass (ie total 5)
    digitalWrite(13, HIGH); // led set to high 
    toggle = 0; // reset toggle
  }
}


void loop() {
  // put your main code here, to run repeatedly:

}