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Links to the same page appear to be ignored in Google's pagerank algorithm.
[edited by: Robert_Charlton at 9:26 pm (utc) on Mar 6, 2013]
I am wondering if anchor links (those with # sign in them) on a website are counted as part of the total number of internal links on a website.
I don't know if this answers your question, but if you look at the Anchor Text area in wmt, there are three different things thrown together in the same "How your data is linked" list. Anchor text from outside; linking text from your own navigation; linking text from intenal # links. You can't tell which is which unless you already know.
I think when you say internal # links, you mean links on a page linking to a specific section of the same page and not links going from one page to another, but I just wanted to make sure?
Navigation links are definitely listed. But then, I don't know how good search engines are at identifying navigation sections. If it's a widely used CMS that comes with something like "id = 'navheader'" then maybe, but otherwise how can they tell?
google will also sometimes show a row of "sitelinks" that are referring to fragment identifiers in the indexed document.
if i had to guess they include the "Jump to" link based on a preponderance of usage in inbound links.