A United States Senate primary run-off election in the deep red Republican state of Alabama would not, in normal times, be a big deal.

But these are anything but normal times, and it is a big deal.

This vote was to decide the Republican candidate for the Senate seat left open by the appointment of Jeff Sessions as US President Donald Trump's Attorney-General.

The casual vacancy was filled by the towering 205cm frame of former Alabama state Attorney-General Luther Strange.

The Republican party establishment wanted Senator Strange to stay in the seat, and Republican Senate leader Mitch McConnell shovelled $US15 million into his campaign to try and seal the deal.

The challenger

Judge Roy Moore is a deeply conservative former chief justice of the Alabama Supreme Court. ( AP: Brynn Anderson )

Senator Strange's challenger was a colourful character indeed — Judge Roy Moore.

Judge Moore is a deeply conservative former chief justice of the Alabama Supreme Court, best known for refusing to remove a monument to the Bible's Ten Commandments from a state building, and promoting conspiracy theories including the "birther" myth that Barack Obama was born in Kenya.

Judge Moore says 9/11 was God's punishment for America's declining religiosity, he says Islam is a "false religion" and homosexuality should be banned.

He drew a pistol from his pocket dressed as a cowboy at a campaign rally on the eve of the election to show his dedication to second amendment gun rights.

Judge Moore rode in on a horse to vote in the Alabama primaries. ( AP: Brynn Anderson )

Judge Moore had the vocal support of former Trump strategist Steve Bannon, Trump foreign policy advisor Seb Gorka, Trump-booster Sarah Palin, and Trump's ideological English cousin, Nigel Farrage, formerly of the UK Independence Party.

So, who do you think Mr Trump was backing?

Actually, it was Senator Strange.

Strange days indeed.

Stranger still is that Mr Trump's man was defeated by Judge Moore by almost 10 points.

Loading

Judge Moore is now the favourite to win the Senate seat against Democrat Doug Jones in December — a Democrat hasn't held an Alabama Senate seat since 1992.

But with a guy like Judge Moore on the ballot, anything could happen. He's considered very politically incorrect — even for Alabama!

Trump not only one riding populist wave

This result is a major blow to Mitch McConnell, whose Republican Senate caucus may be about to get a whole lot more unpredictable — the repeated failure of his attempts to repeal and replace Obamacare prove they are already a pretty unruly bunch.

It also raises the spectre that more incumbent Republican senators facing re-election in 2018 will face primary challengers from populists like Judge Moore, and by "populist" I mean candidates who to many Americans will look like racist nutbags.

But the biggest blow of all may be to Mr Trump himself.

He went against his gut (i.e. Steve Bannon) and supported the "establishment choice" and he lost. Bigly.

Loading

It shows that while Mr Trump rode a wave of popularity fuelled by economic resentment and racial animus all the way into the White House, that wave does not only exist for him, and can carry others a long way too.

Mr Trump now has to decide whether to support those incumbent Republican senators in 2018, or put his chips on insurgents like Judge Moore.

After this humiliating defeat, will Mr Trump continue to side with the establishment which has failed to pass legislation or elect their own members, or run back to the front of the populist parade and reclaim his mantle as their leader?

If he does the latter, the Republican Party — already almost ungovernably split between the Tea Party-backed "Freedom Caucus" and various shades of conservatives from moderates to libertarians — will be in danger of complete dysfunction.

If he does the former, he becomes a traitor to his own cause, and many supporters will see him as a sell-out, just another victim of the Washington "swamp".

After the result in Alabama became known, perhaps we got a clue.

Mr Trump deleted the tweets he had sent supporting Senator Strange.

One thing we know for sure, Mr Trump does not like to lose.