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You could think of a PDF containing a bunch of individual characters, including the spaces and punctuation, that have been individually placed so that they form words. In effect their placement is arbitrary, and when you look inside a PDF it's not always clear what are the words and sentences. Whereas an ebook in MOBI or Kindle format the characters and words are in a continuous stream with a known order. In a PDF the order and placement isn't always as well known. So when a PDF is translated to MOBI the placement isn't likely to be the same as it was in the PDF. Also, in a MOBI and Kindle file there isn't the specific placement like there is in a PDF.
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