The Muslim Brotherhood won by far the largest share of seats allocated to party lists in Egyptian parliamentary elections, final results confirmed on Saturday.

The results gave the Brotherhood and other Islamist groups two-thirds of parliamentary seats and a major role in drafting a new constitution.

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Also on Saturday, the head of the ruling military council announced he had pardoned 1,959 people convicted by military courts in the year since president Hosni Mubarak’s ouster. The list included Maikel Nabil, a pro-Israel blogger whose hunger strike had brought him close to death.

The state Al Nil television channel said the convicts had been pardoned by Hussein Tantawi, the head of the Supreme Council of the Armed Forces, which has ruled Egypt since February.

The pardon comes four days before the first anniversary of the 18-day Egyptian uprising that began on January 25.

The Brotherhood’s Freedom and Justice Party (FJP) has promised that all Egyptians will have a voice in the new parliament, but Islamists are now set to wield major influence over a constitution to be drafted by a 100-person group that parliament will help pick.

Under a complex electoral system, two-thirds, or 332 of the seats in the lower house, are decided by proportional representation on closed party lists. The other third is contested by individual candidates.

According to final results of the staggered election issued by the High Elections Committee on Saturday, the Brotherhood’s electoral alliance took 38 percent of the seats allocated to lists.

The hard-line Salafist al-Nour Party won 29% of list seats. The nationalist New Wafd and Egyptian Bloc coalition came in third and fourth, respectively.

The Revolution Continues coalition, dominated by youth groups at the forefront of the protests that toppled Mubarak, attracted less than a million votes and took just seven of the 498 seats up for grabs in the lower house.

The elections committee did not give results for individual seats, but the FJP’s alliance said on Saturday it now expected to take more than 47% of all seats in the lower house.

Having secured the biggest bloc, the FJP named Saad al- Katatni, a leading Brotherhood official who sat in the old parliament as an independent, as the speaker of the assembly.

While the strong Islamist performance has alarmed liberal Egyptians and Western governments that had close ties to Mubarak, it is unclear if rival Islamists will team up in the assembly.

The FJP expressed its “confidence that Katatni will be at the same distance from all representatives, either those of the FJP or other parties.”

This would “uphold the principle of democracy and consolidate the rules of political participation,” the party said in a statement.

Katatni, who sat on the Brotherhood’s policy committee, told Reuters the new assembly would be “reconciliatory.”

“The priorities are meeting the demands of the revolution, including the rights of the injured and those killed in the uprising,” he said.

The ruling military council also named its choices on Saturday for the 10 parliamentary seats reserved for presidential appointees.

Only two women were among the appointees, something that is likely to further disappoint feminist groups after women won only a handful of seats in the elections. Mubarak had traditionally used the quota to boost the representation of women and Coptic Christians.

Five of the appointees belonged to the Coptic community, which makes up 10% of the population.

Activists said Saturday’s mass pardon of prisoners highlights the Egyptian army’s heavy-handed approach to dissenters who criticize its top generals for using tactics reminiscent of Mubarak’s regime.

Nabil, jailed by a military court for defaming the army, had his prison term reduced to two years from three in December following criticism from international human rights groups. The 25-year-old was arrested in March and began a hunger strike to protest against his conviction for posting remarks saying the army had tried to quell the uprising against Mubarak.

A Coptic Christian, Nabil is a rare pro-Israel voice among Egyptian bloggers. Before his arrest, he released several taped messages directed at Israelis urging them to support the anti- Mubarak revolution.

“We can only say the revolution has succeeded when they release all activists, besides Maikel, who are still being held in military courts, and retry all civilians who have been prosecuted by courts they shouldn’t have been prosecuted by,” Nabil’s brother Mark said.

On Friday, US President Barack Obama stressed Washington’s support for Egypt’s move to democracy and discussed its International Monetary Fund talks in a telephone conversation with Tantawi, the White House said.

“The president reinforced the necessity of upholding universal principles and emphasized the important role that civil society, including nongovernmental organizations, have in a democratic society,” a White House statement said. “He underscored that nongovernmental organizations should be able to operate freely.”

Egyptian authorities swooped in on 17 nongovernmental groups, including the US-funded National Democratic Institute and International Republican Institute, which are both loosely affiliated with the leading US political parties.

Washington was sharply critical earlier this month of raids by Egyptian authorities on prodemocracy groups, but laid the blame on remnants of the Mubarak regime.

Obama and Tantawi also discussed Egypt’s economic outlook.

Egypt has asked the IMF for $3.2 billion in support and an IMF delegation is due to visit late this month.

The country turned down an offer of $3b. in financial assistance from the IMF last June, but since then Egypt’s funding problems have worsened and its currency has come under heavy pressure.