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Associated Press
An Egyptian man votes at a polling center during the third round of the elections for Egypt's parliament, in Qalyobeia, Egypt Tuesday, Jan. 3, 2012.

CAIRO — Egyptians voted Tuesday in the final round of elections likely to seal the domination by Islamists over the country's new parliament as secular activists grew increasingly worried over the possibility of an alliance between the powerful Muslim Brotherhood and the ruling military.

Activists point to what they call mounting signs of a confluence of interests between the Brotherhood, who are set to be the biggest bloc in the next parliament, and the ruling generals. The result, they fear, will be a shelving of reforms for greater democracy that they hoped for after the Feb. 11 fall of President Hosni Mubarak.

"Some very turbulent months are ahead of us," said prominent rights lawyer and activist Negad Borai.

"The military wants a safe return to its past life away from the limelight and with its privileges and prestige, and the Islamists want power. The two have a deal that's at everyone else's expense."

The multistage elections for the 498-seat parliament, the first to be held since Mubarak's ouster, have been the fairest and freest in living memory, a sharp contrast to the large scale rigging and fraud that defined almost every election since army officers seized power in a 1952 coup.

The fundamentalist Muslim Brotherhood, the nation's largest and best organized political group, and the ultraconservative Islamic Salafis have dominated the first two rounds of the vote held since November, together gaining about 70 percent of the vote. That trend is expected to continue in the third and final round, which began Tuesday.

Their triumph has come at the expense of liberal and left-leaning parties and youth groups behind Mubarak's ouster who have since been calling for the military to immediately step down.

At the same time, the military has been waging an increasingly violent crackdown on antimilitary protesters. Last week, soldiers raided 10 non-governmental organizations promoting democracy, including three American groups, raising sharp criticism from Washington.

On Tuesday, the State Department resumed its criticism, saying the military had not carried out promises to stop harassment and return computers and documents confiscated from the groups. "It is, frankly, unacceptable to us that that situation has not been returned to normal," spokeswoman Victoria Nuland said.

"Non-governmental organizations, particularly those who support democracy and a free election process are key part of what the transition to democracy is about," she said, adding that, "We seem to have some Mubarak holdovers in the government who don't seem to understand how these organizations operate in a democratic society and are putting out lots of disinformation about them."

The Brotherhood has denied having any deal with the Supreme Council of the Armed Forces, the group of generals that took power after Mubarak's ouster.

Activists say there are signs of at least an understanding between the two sides over what comes next in Egypt after the elections and the scheduled convening of the new parliament on Jan. 23.

Several major issues dominate the next stage — particularly, what powers the parliament will have, who will oversee the process of writing the next constitution, and how the generals will hand over power, as they have promised to do after presidential elections set for the end of June.