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If by include clause you are talking about SSI includes or PHP, no, both of these output the same text to the browser and that's what the search engine will digest, no problem there.
Lets say you have a file called header.php and it contains the text "this is the header"
you also have a footer page containing "this is the footer"
Within your index page you use the following...
echo"this is the index page";
All the search engine will see is...
this is the header
this is the index page
this is the footer