The maps below show all Victorian lines and the letter prefix assigned to them. It should be noted that whilst all lines are shown, not all lines got automatic signals.

The number was derived from the following formula.
To convert signal number in hundreds of feet to a mileage,
first add 10 (for lines ex Flinders St)
or subtract 48 (for lines ex Spencer St)
before dividing by 52.8".
Note that new installations are being given metric equivilents that do not conform to the above formula.

Some prefixes not shown that were introduced after the map.
ES given to automatic signals on the Melbourne to Albury standard gauge line
NA and SA was used from Sunshine to Deer Park West junction to denote North and South lines
H was used for automatic signals on the up and down middle lines between Richmond and Burnley and on the bi-directional middle line between Burnley and Box Hill
FM was used for automatic signals on the middle line between Caulfield and Moorabbin
MM is a new designation for bi-directional track between Melbourne and Bendigo.
GG was to be used for a proposed track from Tottenham to Laverton, instead it was used for the west line from Newport to Geelong
GGG is used for the Standard Gauge line from Melbourne to Geelong.
Epping line originally had TS but now has T prefix.
Prefix at Dandenong for South East line was originally 'PA', changed to 'X' in 1955. (PA1012 renumbered and relocated to X1012, 3-10-1955)
Prefix at Camberwell for Ashburton/Alamein line was originally 'A', changed to LA in 1955. (When 3 pos signals extended to Hartwell)
CL (Caulfield Local) and CT (Caulfield Through) were used between Hawksburn and Caulfield from 1915 until 1921

If any reader knows of other auto prefix's could you please email me so we can complete the list.
Many thanks to Chris Wurr for supplying the maps and Keith Lambert for additional information.