The Messenger of Allah (ﷺ) used to pray witr with three rak'ahs. In the first he would recite: "Glorify the Name of Your Lord, the Most High" in the second: "Say: O you disbelievers!", and in the third: "Say: He is Allah, (the) One". And he would say the Qunut before bowing, and when he finished he would say: Subhanal-Malikil-Quddus (Glory be to the Sovereign, the Most Holy) three times, elongating the words the last time.
Reference: Sunan an-Nasa'i 1699 In-book : Book 20, Hadith 102 English translation : Vol. 2, Book 20, Hadith 1700
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