Originally, Victory had been a red colour, but Nelson had her, and the rest of the Mediterranean fleet, painted with the stripes. The gunports were painted black, so when they were open it produced a checkerboard effect. This helped the British ships be distinctive in battle amidst the melee of ships and clouds of smoke from the guns, and minimise the risk of friendly fire, as well as being a means to intimidate the enemy. The stripes became the standard for the British navy after that.
When she became a guard ship years later, she was painted in black and white stripes. Years later still, as a tourist attraction, she was repainted to Nelson's colours.
But the experts have discovered, by peeling away an incredible 72 layers of paint in places, that it might not be in Nelson's colours at all. That the current 'orange' would in fact have been a paler ochre colour.
There are plans to repaint the Victory to more closely resemble the ship that Nelson knew, however there is still more research to do to make sure it is as accurate as it can be.
Source: http://www.portsmouth.co.uk/news/defence/historic-paint-traces-may-reveal-the-true-colours-of-nelson-s-flagship-hms-victory-1-5951194
