I’ve restored the .htaccess file from my backup. Now it’s working fine…
If anyone facing the same problem have a look at the new .htaccess file
# BEGIN WordPress
RewriteRule ^index\.php$ - [L]
# uploaded files
RewriteRule ^files/(.+) wp-includes/ms-files.php?file=$1 [L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule . index.php [L]
# END WordPress