Updated

President Obama on Monday said Iranian voters have a right to feel their ballots mattered and urged the investigation into vote-rigging allegations to go forward without additional violence, and the State Department announced that the U.S. is "deeply troubled" by the latest news from the scene.

Tens of thousands of Iranians took to the streets in Tehran and other cities, defying a country-wide crackdown to protest the outcome of Friday's presidential election, which declared Mahmoud Ahmadinejad the victor over Mir Houssein Mousavi.

Iran's Supreme Leader Ayatollah Ali Khamenei, who is the ultimate power in the country, has decided to investigate charges of fraud.

Obama said reports of violence that followed Iranian elections trouble him and all Americans. He said peaceful dissent should never be subject to violence that followed weekend elections that gave Ahmadinejad a second term.

"It would be wrong for me to be silent on what we've seen on the television the last few days," Obama told reporters at the White House.

Obama said he had no way of knowing the results were valid -- he said the United States had no election monitors in the country -- but it was important that the voters' choices be respected.

State Department spokesman Ian Kelly told reporters that the United States is concerned about allegations of ballot fraud, though it knows too little about the conduct of the election to say whether fraud occurred. He declined to "condemn" the Iranian security forces for their crackdown on street protesters, saying analysts are still assessing the situation.

White House Deputy Press Secretary Bill Burton paraphrased Vice President Joe Biden, telling FOX News that the United States will deal with the government that emerges in Tehran, not the one the Obama administration would want.

"The United States deals with the facts. And the fact is we're going to take whatever leadership there is in that country and try to pursue our goals and objectives and that means dealing with the Iran that we've got, and not the Iran that we wish we had," he said.

Biden said Sunday that he was doubtful the elections were free or fair, but the United States maintains its goal of stopping terrorism and the development of nuclear weapons in Iran

Burton said the United States is concerned about what has happened, but the Obama administration is withholding judgment on the outcome of the election. He said officials are "observing, trying to get as much information as we can get."

Burton also tried to cast the outcome in the best possible light.

"Obviously, we are encouraged by the amount of participation and the enthusiasm in the vigorous debate, especially among young people in that country. And we are going to continue to pursue our goals in the region which include making sure that Iran does not get a nuclear weapon and that they stop terrorism," he said.

Separately, Burton defended President Obama's peace envoy to the Mideast, Dennis Ross, who Israeli media reported Monday is on the outs and will be reassigned. Sources who spoke with Ha'aretz newspaper suggested that Ross' Jewish roots and strong sources with the Israeli government made him unacceptable to Ahmadinejad.

The president "continues to have confidence in him moving forward," Burton said of Ross, noting that "one of the things that Dennis Ross proposed actually was pursing strategic objectives with Iran while at the same time pursuing peace between Israel and Palestine, both on two tracks but at the same time."

Click here to read the Ha'aretz article on Dennis Ross.