Secretary of State Kathy Boockvar said the process to count provisional ballots is now underway.
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Boockvar said the county boards of election will have to individually evaluate each provisional ballot and decide within seven days if it meets the standard to be counted.
That will be done by verifying the voter was registered to vote in the precinct the ballot was cast, and that the voter did not cast a mail-in ballot before requesting a provisional ballot at a polling place.
The eyes of the nation remained on Pennsylvania Friday to see which of the presidential candidates will receive the state's crucial 20 electoral votes.
Former Vice President Joe Biden pulled ahead of President Donald Trump on Friday morning, and the lead steadily grew throughout the day.
In Philadelphia, a bipartisan panel of commissioners said they are focusing on accuracy and transparency. About 40,000 ballots remained to be counted in the city.
"We are fortunate to have that machinery to allow us to count faster, but it's still is a process. So we get all these envelopes in and it's like an assembly line," said Commsisioner Lisa Deeley.
In Pennsylvania, mail-in votes were accepted until 5 p.m. Friday as long as they were postmarked by Election Day.
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All week, the Philadelphia commissioners have said mail-in votes received after Election Day, but by the Friday deadline, would be separated into a different pile and won't be counted just yet.
The wait to count those ballots comes from guidance issued by Boockvar.
But, on Friday, state Republicans asked the U.S. Supreme Court for an emergency order to ensure that no late-arriving mail ballots are added to the totals.
In the attached filing, the GOP argues that Boockvar's guidance is non-biding on county boards and claims that 25 of 67 counties haven't indicated whether or not they are abiding by it and in fact segregating the late-arriving votes.
On Friday evening, Justice Samuel Alito issued an order requiring all Pennsylvania counties to abide by the non-binding guidance from Boockvar that they segregate late arriving mail ballots that are being challenged by Republicans.
Alito also says he's going to urge his colleagues to conference on the pending petition ASAP.
"I am immediately referring this application to the Conference and direct that any response be filed as soon as possible no later than 2pm tomorrow, Nov. 7," Alito wrote.
Also in court Friday, a statewide appellate court judge dismissed a request from Republicans to stop counties and the state from counting provisional ballots cast by voters with disqualified mail-in ballots due to a technicality.
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Democratic Gov. Tom Wolf's state elections bureau last month told counties voters could use provisional ballots if they "did not successfully vote" with the mail-in or absentee ballot they had been issued, or if their ballot had been rejected and they believed they were still eligible to vote.
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The Trump campaign also tried to stop the count in Philadelphia itself - alleging city officials were depriving their observers of meaningful access - but a federal judge refused to go along, instead urging the sides to forge an agreement.
Speaking from the White House on Thursday night, Trump made unsupported allegations that Democrats in Pennsylvania and elsewhere were trying to steal the election.
It was unclear whether any of the legal challenges would make a difference to an eventual outcome.
More than 2.6 million mail-in ballots were cast, and there has been no report of fraud or any other problem with the accuracy of the count.