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The defeated candidate in Indonesia's presidential election is expected to file a court challenge to the result as calm returned to the capital Jakarta following a 24-hour spasm of apparently orchestrated violence.

The campaign team of former general Prabowo Subianto has said it will file a challenge to the Constitutional Court on Thursday.

Six people died in rioting that started Tuesday night after official results confirmed President Joko Widodo had won 55.5% of the vote in the April 17 election, securing him a second term.

Subianto has refused to accept the result, instead declaring himself the winner and alleging massive fraud.

The election supervisory agency earlier this week rejected Subianto's complaint about the election's integrity after the only evidence of fraud provided by his team was links to online articles.