The code goes like so:
while the pattern matches what is in $seq
   assign $start the value of the length of the whatever is left in $seq after what was currently matched ($').

the explaination of the pattern using japhy's Yape::Regex::Explain module goes as follows:

The regular expression:

(?-imsx:/(ATG)(...)*?(?=TAA|TAG|TGA)/og)

matches as follows:

NODE                     EXPLANATION
----------------------------------------------------------------------
(?-imsx:                 group, but do not capture (case-sensitive)
                         (with ^ and $ matching normally) (with . not
                         matching \n) (matching whitespace and #
                         normally):
----------------------------------------------------------------------
  /                        '/'
----------------------------------------------------------------------
  (                        group and capture to \1:
----------------------------------------------------------------------
    ATG                      'ATG'
----------------------------------------------------------------------
  )                        end of \1
----------------------------------------------------------------------
  (                        group and capture to \2 (0 or more times
                           (matching the least amount possible)):
----------------------------------------------------------------------
    .                        any character except \n
----------------------------------------------------------------------
    .                        any character except \n
----------------------------------------------------------------------
    .                        any character except \n
----------------------------------------------------------------------
  )*?                      end of \2 (NOTE: because you're using a
                           quantifier on this capture, only the LAST
                           repetition of the captured pattern will be
                           stored in \2)
----------------------------------------------------------------------
  (?=                      look ahead to see if there is:
----------------------------------------------------------------------
    TAA                      'TAA'
----------------------------------------------------------------------
   |                        OR
----------------------------------------------------------------------
    TAG                      'TAG'
----------------------------------------------------------------------
   |                        OR
----------------------------------------------------------------------
    TGA                      'TGA'
----------------------------------------------------------------------
  )                        end of look-ahead
----------------------------------------------------------------------
  /og                      '/og'
----------------------------------------------------------------------
)                        end of grouping
----------------------------------------------------------------------
[download]

as for the modifiers /og on the pattern take a look at perldoc perlop.

Anyhow, hope this helps.

-enlil