Error on rewrite rule inside subdirectory - .htaccess

Question

When my website was inside the root directory of my hosting, everything works find. However, I had to move my website files to a subdirectory.
Old:
/www/*
Current:
/www/websites/example
Now, I can visit the homepage of my website, but I get error when I visit other pages of my site.
example.com/1234/title_of_url -> example.com/index.php?qa-rewrite=1234/title_of_url
But when I visit that sample page, i get the following error.
Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator and inform them of the time the error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Here is my .htaccess file:
RewriteEngine On
RewriteCond %{REQUEST_URI} ^(.*)//(.*)$
RewriteRule . %1/%2 [R=301,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^.*$ index.php?qa-rewrite=$0&%{QUERY_STRING} [L]
Note: I have moved the file to my /www/ dir and it works fine. So I think I am missing to put websites/example somewhere in my .htaccess

Answer 1

Use this rule in site root .htaccess:
RewriteEngine On
RewriteCond %{REQUEST_URI} !^/websites/ [NC]
RewriteRule .* websites/example/$0 [L]
Then use this code in websites/example/.htaccess:
RewriteEngine On
RewriteBase /websites/example/
RewriteCond %{REQUEST_URI} ^(.*)//(.*)$
RewriteRule . %1/%2 [R=301,L,NE]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(?!index\.php$).*$ index.php?qa-rewrite=$0 [NC,L,QSA]