Heavy rain will hit parts of Scotland again as unsettled weather continues to cause travel disruption. 

The borders, the south-west of the country and parts of the east coast are expected to be hammered by rain this afternoon. 

The Met Office confirmed a yellow warning covering the area will be in place from 3pm until 11.45pm on Thursday. 

Flooding at Moncrieffe Tunnel could make the tracks unstable (Image (L): Network Rail)Met Office

An earlier warning was in place until 10am this morning with the downpour resulting in flooding on rail lines at "several locations". 

Network Rail Scotland confirmed multiple closure of the lines due to the flooding south of Hilton Junction near Perth. 

Just south of Perth at Moncreiffe Tunnel the heavy rain saw a "waterfall" form with water pouring down the sides of the structure. 

The intense water has increased the risk of the ballast, or stones which hold the rails in place, shifting and could possibly make the track unstable. 

A statement from the rail infrastructure bosses added that the line was closed between Hilton Junction and Ladybank in both directions.

The line is also shut north from Gleneagles. 

It later added: "We've now had to close all lines south from Perth, following reports of fast flowing water coming down an embankment."

In the most recent announcement, Perth station was also closed due to flooding.

The most recent weather warning also warned of "flooding in a few places".

A statement from the forecasters read: "A period of heavy rain is likely later this afternoon and evening, perhaps with thunder close to the east coast.

"10 to 15 mm may fall within an hour in a few spots, while more widespread totals of 20 to 30 mm seem likely over 3 to 6 hours.

"Some hillier parts, perhaps especially across Lothian and Borders, could perhaps see around 50 mm, this falling onto wet ground, increasing the possibility of a few flooding problems."