HPP is a programm to suggest wich part of a given polypeptid is likely to to reside in the membran or in the cytosol. This means that a high positive peak indicates a big prababilty that this peace of the protein resides outside the mambrane and the part with the negative values resides inside it. But you can not compare the predictions made for different sequences. The curves are scaled to fit on the screen and and the y-axis is not labeled. This got to do with the clipboard.
Some browsers do clip the content of the clipbard when pasting it into an textarea of an applet.
Because pieces of text containing the sequence of a protein can be pretty big this would not work. You can do this in two ways. You also can paste pdb.-files, HPP will extract the seqeuence on the fly. Please notice that this will replace the content of the input-field. Choosing the method of calculation.