Senate Republicans are at odds with President Trump Donald John TrumpBubba Wallace to be driver of Michael Jordan, Denny Hamlin NASCAR team Graham: GOP will confirm Trump's Supreme Court nominee before the election Southwest Airlines, unions call for six-month extension of government aid MORE over Roy Moore and the Alabama Senate race.

Trump broke more than a week of silence on Tuesday by raising doubt about the allegations of sexual misconduct facing Moore, contradicting Senate Majority Leader Mitch McConnell Addison (Mitch) Mitchell McConnellGraham: GOP will confirm Trump's Supreme Court nominee before the election Trump puts Supreme Court fight at center of Ohio rally The Memo: Dems face balancing act on SCOTUS fight MORE (R-Ky.) and other Senate Republicans.

Trump pushed back on a reporter who asked how he felt about electing a “child molester” by noting that Moore “totally denies it.”

The Alabama Republican became embroiled in scandal after The Washington Post reported that he initiated a sexual encounter with a 14-year-old girl when he was 32.

Several other women have come forward to accuse Moore of inappropriate sexual advances that happened when they were teenagers.

“He says it didn’t happen, ”Trump told reporters on the South Lawn of the White House. “You have to listen to him, also.”

That’s not what McConnell wanted to hear, according to sources close to the Senate GOP leadership.

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McConnell is worried that Moore will drag down Republican candidates in 2018, which is shaping up to be a tough year for the GOP, and will hurt the party’s brand.

“Not only does Moore really hurt Republicans in the Senate and Republicans nationally, he also does great damage to the conservative movement because now every conservative has to answer for Roy Moore,” said a strategist close to the Senate Republican leadership.

“Roy Moore comes along, claiming to be a conservative, and now all conservatives are saddled with a guy who is known for one thing and that’s assaulting kids,” the source added.

McConnell’s top priority is keeping Republicans in control of the Senate after 2018 and some GOP strategists believe that will be tougher with Moore in the Senate.

McConnell told reporters last month that he keeps in mind the lesson of former Rep. Todd Akin (R-Mo.), who became an embarrassment to the party in 2012 by talking about “legitimate rape.”

Akin not only lost a Missouri Senate seat that the GOP appeared poised to win but he hurt Republican candidates in other states.

“You don’t have to be the most astute to read the exit polls out of New Jersey and Virginia and look at the results around the country to realize women, people of color and voters younger than 40 are moving in a tidal wave against the Republicans. So why would you want, going into 2018, to embrace or be handcuffed to Roy Moore? Why?” said Republican strategist John Weaver.

“At least McConnell and them are smart enough to get that,” he said.

But Trump appears less concerned with how the Alabama race may affect contests next year in Nevada, Arizona, Pennsylvania and other battleground states, and more focused on getting his legislative agenda passed over the next 13 months.

"I can tell you one thing for sure, we don't need a liberal person in there, a Democrat, Jones," Trump said this week. "I've looked at his record— it's terrible on crime. It's terrible at the borders.”

Trump’s senior advisor, Kellyanne Conway, when asked about Moore on Monday, said: “we want the votes in the Senate to get this tax bill through.”

State officials say the race won’t likely be certified until Dec. 26, giving Senate Republicans a chance to pass tax reform legislation and a negotiated compromise with the House before Moore or his Democratic opponent, Doug Jones, takes the oath of office.

But there are other priorities for which Trump will need as many Republican votes in the Senate as possible: immigration reform, an infrastructure package, deregulation of the financial services industry, to name a few.

“I think Mitch McConnell would love to figure out a way to kick him off the ballot and the White House is resigned to him not getting off the ballot,” said Jim McLaughlin, a Republican consultant who has done a lot of political work in Alabama.

“Mitch McConnell is saying let’s try to get this guy off the ballot. Down in Alabama, the only politician to come out against him is [Sen.] Richard Shelby Richard Craig ShelbySenate GOP eyes early exit Dems discussing government funding bill into February GOP short of votes on Trump's controversial Fed pick MORE [R-Ala.]. All the other local politicians say let the people decide,” he added.

A second GOP strategist close to Senate GOP leaders, who requested anonymity to speak about the president candidly, said it made sense for Trump not to side with Moore’s accusers because he is facing allegations of inappropriate behavior from at least 13 women.

One accuser, Summer Zervos, who appeared on Trump’s reality television show, “The Apprentice,” has filed a lawsuit that may come before the New York Supreme Court.

Trump’s comments put pressure on the Republican National Committee and the National Republican Senatorial Committee, which both cut fundraising ties with Moore, to spend some money to help him win the race.

Spokespeople with both committees did not respond to requests for comment about Trump’s statement.

Republicans in Alabama say Trump’s response to the allegations against Moore more closely reflects the sentiments of Alabama voters.

A Raycom News Network poll of 3,000 likely Alabama voters this week found that Moore has a two-point lead over Jones and 48 percent of Republicans do not believe the allegations against Moore.

Some Alabama voters still remember Republican candidate Steve Windom’s race for lieutenant governor in 1998 when he was accused by a former prostitute of rape and sodomy. The accuser, Melissa Myers Bush, later admitted in court that she accepted money to make false allegations.

Windom won the race despite the false charges, becoming the first Republican lieutenant governor of the state in more than a century.

“Donald Trump and the GOP establishment haven’t been on the same page,” said Jon Gray, a GOP consultant based in Alabama who has polled the Senate race frequently.

Gray says that even though Trump is from New York and has spent a lot of time in Florida, “he really does think like Alabamians think.”

“He gets it,” he added.

While McConnell and other Senate Republicans have been quick to side with the women accusing Moore of misconduct, many Alabama voters are giving him the benefit of the doubt.

The Raycom poll showed that “only 29 percent of the entire state believe all of the allegations,” Gray noted, “that’s not even one in three and that’s Democrats and Republicans together.”

Trump won Alabama with 62 percent of the vote in last year’s general election and it gave him a dominating victory in the Republican presidential primary. He more than doubled the vote total of his nearest competitor, Sen. Ted Cruz Rafael (Ted) Edward CruzThe Hill's Morning Report - Sponsored by Facebook - Washington on edge amid SCOTUS vacancy Murkowski: Supreme Court nominee should not be taken up before election Battle lines drawn on precedent in Supreme Court fight MORE (R-Ala.).

Trump ended his thank-you rally tour with a big event in Mobile in December.