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Morsi's supporters have camped out in two areas of Cairo since shortly before Morsi was ousted, and hundreds marched Wednesday to the Cabinet building in central Cairo to denounce the new government, which was sworn in on Tuesday.
Mansour also has announced a road map for the transition to democracy, including a loose schedule for rewriting the country's constitution, suspended after Morsi's ouster, and electing a new president and parliament.
His political adviser Mustafa Hegazy said Wednesday the transition would be completed in around nine months. Addressing concerns about the Brotherhood's exclusion from the political process, Hegazy said the military-backed administration would launch an initiative aimed at starting a transitional justice and reconciliation process next week.
The Arab world's most populous country has had a rocky transition following the 18-day popular uprising that removed Mubarak from power in 2011. The euphoria at the end of Mubarak's nearly 30-year rule was dampened as the political divisions deepened, the economy plummeted and crime soared.
Since Morsi's election, Egypt's politics grew more polarized, split into two camps, with secular Egyptians, liberals, Christians and moderate Muslims accusing Islamist leader of giving the Brotherhood undue influence. The fault lines deepened after Morsi's ouster, except that the Islamists are no longer in power and growing as entrenched as the opposition.
Morsi and his supporters maintain that his rule has been sabotaged by Mubarak loyalists eager to regain power, an opposition that had no genuine interest in reconciliation and a seemingly endless series of strikes, protests and street violence.
On Wednesday, demonstrators carried posters of Morsi and chanted slogans against the military in a march to the Cabinet building, near Tahrir Square, where Morsi's opponents have been camped out since before his ouster.
Security forces barred them from reaching the Cabinet building, but protesters painted graffiti on the walls calling el-Sissi a killer and traitor. They also appealed to the military's rank-and-file, saying the senior officers who carried out the coup were "sowing the seeds of division between the people and the army."
After late-night prayers Wednesday for Ramadan, small groups of pro-Morsi protesters held rallies outside the country's Supreme Court in Cairo and outside the presidential palace and the Republican Guards club. There were also small protests in southern Egypt by a few hundred Morsi supporters. All of the rallies dispersed peacefully and swiftly.
Also Wednesday, militants fired at a conscript on duty outside a police station in North Sinai's capital, el-Arish, killing him, security officials said. The officials spoke on condition of anonymity because they were not authorized to address reporters. They said the 23-year old conscript was killed by snipers.
Violence in Sinai has increased following Morsi's ouster, as militants target police stations and security forces, some vowing to drive the military out of the peninsula.