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The ATMEGA88 Datasheet has two pins for PD5 on page 3 for the TQFP layout. Those pins being Pin 9 and Pin 12. Normally, I wouldn't blink twice, but It seems that both pins have different functions. Is this a typo, or intentional?

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Pin 12 very likely is PB0. Check page 64.

This Atmel datasheet and the Microchip datasheet and this one confirm.

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