In the second essay in The Genealogy of Morals, Nietzsche begins by noting how the development of morality seems to be leading towards some final end. The paradoxical task that humanity has set for itself is to keep promises. Promising requires making a memory of the will. But humans have an active capacity for forgetting, which hinders our ability to make promises. The person who can make and keep promises is the sovereign individual. The sovereign individual is someone who lives a life with a certain organization or order. This allows him to know what promises he can make and keep. He also knows himself well enough to predict whether he will be able to keep a promise. In addition, the sovereign individual can identify causes and effects, allowing him to perform calculations necessary for making and keeping promises. He also judges himself according to no standards other than his own. In other words, he is his own measure.
The sovereign individual calls his own dominating instinct his 'conscience'. Guilt, or what Nietzsche calls 'bad conscience' has another origin: the creditor-debtor relationship. Nietzsche says that in earlier societies, sacrifices were made to ancestors in order to attempt to repay a debt. We owe our forefathers something because they created the society in which we live. The more powerful a society gets, the larger this feeling of debt becomes. Eventually, ancestors are thought to be so powerful that they are given some kind of divine status. This reaches a peak with the conception of an all-powerful, perfect god of the Judeo-Christian tradition. The debt owed to an all-powerful God can never be repaid; this is why the debt gets internalized as a feeling a guilt. Nietzsche notes that in German, Schuld is the word for both guilt and for debt. If you think about it, both conscience and bad conscience are ways of calculating and measuring ourselves in comparison to others or to ourselves.