Direct comparison of RS1140646 with part of chromosome 22
Forget SNPs. Forget CG-dinucleotides. Your focus now is on just a pair of sequences: RS1140646 and the region in chimp chromosome 22 it looks like it matches. Maybe Blast got confused by the necessity of finding the 21 nucleotides in a sequence of 47 million nucleotides. If so, you'll make it real simple.

You are going to ask Blast to do a pairwise comparison of RS968436 and RS1140646 against their corresponding sequences in chromosome 22, just the several nucleotides with no chance for confusion by extraneous chimp sequences. You can see with your own eyes that the two pairs are equally good matches. Unless the Blast has gone crazy, it will agree.

First you run a pairwise comparison of RS968436 and it's match [which you can copy and paste from the inset two slides ago]... That is very good.

Now you try RS1140646 and its match, very carefully -- no sudden motions --- so as not to give the Blast any cause for...

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