“DON’T let the Scots keep you in Europe” was the key message from the Leave campaign as Britain’s voters decided on the country’s membership of the EU.

In an email to supporters, Matthew Elliott from the campaign warned his fellow Brexiteers that the Scots were voting in big numbers.

And Scotland and London, Elliott suggested in the message, were not part of the “heartlands of the country”.

“We’re hearing reports that the two areas of the country most against us – SCOTLAND and LONDON – are voting in big numbers,” Elliott wrote.

He continued: “There is a very real chance that voters in London and Scotland will vote to keep us in the EU today despite the heartlands of the country voting to leave”.

He added: “If you don’t want people in London to force you and your family to stay in the EU please email and call all your friends and make sure they Vote Leave today!”

Scotland Stronger In spokesman Kevin Pringle tweeted: “So here we have it from official @vote_leave: Scotland (and London) are not “heartlands of the country”! #VoteRemain.”

Labour MP Chuka Umunna, a member of the official Remain campaign, said the message was divisive, describing it as “utterly disgraceful”.

Meanwhile, there was a worry that flooding and heavy rain in parts of England may have hampered turnout.

Though there was, what Nicola Sturgeon described as “perfect voting weather” in Glasgow, many thousands of commuters in London were caught up after weather disrupted some of the city’s busiest tube and train stations.

Some reports suggested a month’s rain had fallen in the space of a few hours.

Network Rail said it had 1,200 engineers working on weather-related issues across the network.

The Met Office had issued an amber “be prepared” warning of rain for parts of the south east of England. Forecaster Luke Miall said: “If you draw a line from The Wash to the Isle of Portland, everything east of that is in the firing line.

“A band of showers is coming across the English Channel and moving north-eastwards; that will bring some heavy downpours and localised surface flooding.

“There’s going to be a bit of hail in there too, so there’s quite a lot going on.”

In Glasgow, the First Minister told voters outside the Broomhouse Community Hall, that she was “really optimistic” about the result.

“From what I could see on social media the weather is very patchy across the UK. I saw reports of people turning up to vote in pouring rain, but it’s blue skies and sunshine in Glasgow – as always – so it’s perfect voting weather.”

Scotland’s chief returning officer, Mary Pitcaithly, was equally confident that Scots had turned out in great numbers, telling the BBC she expected the final figure to be between 70 and 80 per cent.

Though unlikely to match the 85 per cent turnout in the 2014’s Scottish independence referendum, Pitcaithly said she thought it was likely to be greater than the 56 per cent who voted in May’s Holyrood elections.

Each of Scotland’s 32 local authorities had their own count, with Pitcaithly, Falkirk council’s chief executive, responsible for tallying them all and announcing the result for the whole of the country early this morning.

Prominent leave campaigner Boris Johnson was also in Scotland, where he attended his daughter’s graduation at St Andrew’s University. The former Mayor of London may have stolen the limelight from eldest child Lara Johnson-Wheeler when he unveiled a “last chance to vote” poster during the hour-long ceremony at the university’s Younger Hall.

Reports suggested that, later in the ceremony, a student unveiled their own “Remain” message as they collected their degree, pointedly waving it in Johnson’s direction.

A witness to the stunt told the Daily Record: “It was all done very much tongue in cheek. Both posters got a huge cheer and round of applause. Boris wasn’t telling people who to vote for, just for them to get out there and make the effort.”

In the dying moments of the referendum, Johnson made one last push for voters, emailing supporters: “Polls close in 90 minutes, so obviously we don’t have time for long emails. If you have voted leave, thank you. If you haven’t yet, please do. And please email, text or phone all your friends to Vote Leave.

“Don’t lose this chance to make today our Independence Day!!! Thank you so much.”

It ended: “Sent from my iPhone”

Meanwhile, the man tipped for a position in a future post-Brexit Boris cabinet, Ukip leader Nigel Farage, insisted his side would win if “soft” Remain voters stayed home.

“Actually I do think we are in with a very strong chance, I do genuinely. But it’s all about turnout and those soft Remainers staying at home.

I do think that the people who have decided to vote Leave have a real conviction and passion,” Farage said.

Later in the day. Farage took to Twitter writing: “If you want your borders back, if you want your democracy back, if you want your country back then vote to leave! #IndependenceDay.”

Tory MP, Remain supporter and grandson of Winston Churchill, Sir Nicholas Soames, replied scathingly: “Oh bollocks.”

Prime Minister David Cameron ignored questions about the weather, saying only “Good morning” to the reporters as he and wife Samantha voted in Westminster.

Labour leader Jeremy Corbyn was exceptionally positive when he vote in his Islington constituency in north London. Asked if he was feeling confident, Corbyn smiled and said: “Extremely, it’s a very good day.”

On the outcome of the referendum, he joked: “You could either check the wind or check the bookies. The bookies usually get it right.”

But he then pointed out that they had got it wrong about him and the Labour leadership.

Pro-Leave Justice Secretary Michael Gove said he was feeling “quite excited” as he accompanied his wife, Sarah Vine, to a polling station in North Kensington.

The markets seemed to be predicting a Remain vote, with the pound at a new high for the year and shares up. It was a volatile day’s trading with the pound and FTSE100 surging in the morning, falling back in the afternoon and then rallying again later. That domestic confidence was also reflected globally with investors taking the view that Brexit was unlikely.

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Michael Hewson, chief market analyst at City firm CMC Markets, said: “The FTSE 100 has gained nearly 7% in the last seven days while the pound has rebounded from lows of 1.4010 to peak earlier today at 1.4950 and post its highest levels this year, as the polls continue to improve in favour of remain.

“This suggests that a good part of this remain bounce could well be largely priced in already and if we get some early results in the early hours of the morning pointing to a move back to the leave camp then sterling could drop back sharply, potentially dragging stock markets down too.”

One of the slightly odder occurrences on polling day was the brouhaha over how people should make their mark. There were reports of Leave supporters being told to take pens to avoid MI5 agents rubbing out their pencil crosses ballot papers.

A poll this week suggested two-thirds of Ukip voters believe the government are going to rig the referendum result, while a third of them believe MI5 are involved.

There were numerous tweets and messages between Brexit activists urging them to use pens.

Although pencils are provided in polling stations, there is no legal reason why a voter cannot use a pen. Councils tend to use pencils because they are significantly cheaper.

Though East Northants council upset some people when they suggested that using a pen could smudge the ink. They tweeted: “Please use a pencil on your ballot paper as ink can smudge when its folded which could make the paper doubtful & it may not be counted.”

One Ukip supporter claimed remain campaigners had called the police on her because she was offering fellow leave voters her pen.

A spokesman for Sussex police said they had been called to the polling station, in Durnford Close, by a volunteer who reported a disturbance, but that no offences had been committed and it was not being dealt with as a police matter.