I am trying to redirect multiple drupal sites to same code base using following htaccess file

RewriteEngine on
RewriteCond %{HTTP_HOST} ^(www.)?site.com$ [NC]
RewriteCond %{REQUEST_URI} !^/subdirectory/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ subdirectory/$1
RewriteCond %{HTTP_HOST} ^(www.)?ngeneric.com$ [NC]
RewriteRule ^(/)?$ subdirectory/index.php [L]

It workds but, now every URL on the site has its subdirectory infront like

http://site.com/**subdirectory**/.....

How to fix this?

More Info: Domain is routed to public_html/a/ The drupal site in inside this a directory as public_html/a/b and I am trying to use multiple sites, so I am getting this problem.