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I have a Flask application. I use multiple subdomains in this application. I created a web application named www.mydomain.com. I ran my application here. I added the CNAME record given in the www.mydomain.com web application for www, subdomain1 and subdomain2 to my domain provider. When I enter www.mydomain.com, the pages belonging to the www subdomain open. However, when I enter subdomain1.mydomain.co, the PythonAnywhere Coming Soon page opens.

For each subdomain on PythonAnywhere you'd need a separate web app.