The horizontal sequence is a human 3' EST coding for an unidentified protein (well, it has now been identified, but let's pretend it had not...). The vertical is the protein sequence of the closest BLASTX match, in this case a mouse granulocyte colony stimulating factor receptor precursor (whew! :-).
As we can see from the graph, the EST matches the C-terminal part of the protein and contains a 3'-UTR. The diagonal is not perfect, however: there are two partial diagonals but the C-terminal one is shifted one position downstream with respect to the first one. This is a clear sign of a frameshift. The alignment window shows this well: there is a rather good match on frame 1 but it starts at position 806 or so (in the protein sequence).


If we move the protein sequence one residue upstream, we get another good match, but this time on frame 3, and it extends only through position 792 (of the protein sequence). It might seem strange that the match on frame 1 doesn't start where the match on frame 3 ends, but this is due to sequence divergence, not to the frameshift..


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