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Thein Sein said government officials and the Karen rebels are holding informal talks. Mrs. Clinton earlier offered U.S. assistance to facilitate a peace process.

Communal violence in Myanmar’s western Rakhine state also is posing a challenge for the government. Rohingyas, who are stateless Muslims, have been raped, arrested and killed by Myanmar security forces following deadly clashes with majority Buddhists in June.

Thein Sein said the violence is unfortunate and unexpected, but that a commission has been established to investigate.

In her meeting with Thein Sein, Mrs. Clinton expressed appreciation for “what he has done, especially in terms of transforming the political landscape that is Burma today,” said the senior State Department official. Myanmar was formerly known as Burma.

There are still more than 300 political prisoners in Myanmar.

Mrs. Clinton and Thein Sein discussed the release of all political prisoners and the conflict with ethnic minorities in Myanmar. She also urged Myanmar to end its military relationship with North Korea.