When creating a new counter you can set the starting value by adding a count parameter to the URL. So if the counter "qwerty" didn't exist, accessing the URL
http://www.med.kagawa-u.ac.jp:80/~genomelb/takezaki/poptree2/cgi-bin/countcgi.pl?qwerty&COUNT=1234
will create a new counter called "qwerty" with its counter set to 1234.
The counter can only be set when creating a new counter.