Optimizing a JavaScript Site for Search Engines - Content Positioning
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3. Content Positioning
Large sections of JavaScript can also have the same effect as tables. The search engine attempts to read this information first, which causes the normal HTML text to appear lower on the page.
Search engines read web pages from top to bottom, just like you or I do. However, search engines place a greater weight on text at the top of the page than at the bottom. When you have great amounts of JavaScript that pushes the content way down on the page, this can reduce your relevancy score.

Figure-4
Notice in the picture how far down the actually body of the page is. Also notice the scrollbar on the side; this tells you that the body of the page only comprises the lowest 1/5th of the page. What this means to the search engines is this: Whatever you had to say at the top of the page is more important than what is at the bottom; since the search engine spider cannot read what is supposed to be “important,” it assumes that your relevancy to search queries is not enough to list in the SERPs, and probably will not even list you there.
Some “expert” SEOs have determined that simply placing the JavaScript near the bottom of the page has a better impact on the way that the code is scanned. While initially the content positioning is important, it still does not minimize the work the spider has to do. There is no way for the search engine spider to know that there isn’t more content below the JavaScript, even if it is on the bottom of the page.
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