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This will be McFarlane's third term in the job. She campaigned on a platform of economic development for all, growing downtown, and boosting transit.
"It's really time for us to start working as a team. As mayor, I challenge each of us to collaborate and cooperate and move things forward," said McFarlane in her victory speech.
She said she looks forward to working on issues like transportation and working past things like the new patio rules for restaurants that the council put into place in August.
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"Talking to businesses down here, really the overall message is downtown is so much more than that, Raleigh is so much more than that and it's kind of disappointing that that became such a central key," she said.
Watch: victory speech
In a concession statement, Welzin thanked his supporters for their hard work.
"...though we are disappointed that the count was not in our favor, it is impossible to not reflect proudly on this race," he said.
Durham and Fayetteville also held municipal elections Tuesday. Voters there were narrowing the field of candidates for mayor ahead of the next election November 3.
In Fayetteville, incumbent Mayor Nat Robertson and former City Councilwoman Val Applewhite will face off in November.
In Durham, incumbent Mayor Bill Bell will face challenger James Lyons in November.