The port that the source database uses is usually configured in parameter files, scripts (if scripts are used to start the database), or within the <DLC>/properties/conmgr.properties file if the database is started by the AdminServer.
The source database initiates connection to the target so the source can use any port the DBA defines for the -S parameter.

The source database looks within a file named <dbname here>.repl.properties this file must be in the same directory as the database.
If the database name is sports2000 then the replication properties file would be named sports2000.repl.properties.

Within the <dbname>.repl.properties file will be one or two agent definitions depending if one or two replication targets will be configured.
The sections for each agent will look similar to the following:
[control-agent.agent1]
   name=agent1
   database=target
   host=localhost
   port=4501
   connect-timeout=600
   replication-method=async
   critical=0

Within this definition of the first agent is the definition of "port=".
In the above example the port that the replication target is expected to be listening on is 4501.
This may be altered to whatever is the correct port that the target will be configured to run and listen on.

If working with replication sets then each of the databases will need to be configured similarly to set the correct port for the database on the correct host (if more than one machine is used).