LetŐs look at Hars2 in more detail by mapping all of the perfect match probes (16 of them) that target this transcript.
	Go back to the Trait Data and Editing window and select Chr 2 (rather than ALL as shown above) and also select PM Probes. Then click on Interval Mapping button.
	You will get the illustration above, but without the sequence data that we have added.  The 16 perfect match probes are arranged in sequence (red is 5 prime, blue is the 3 prime end). For example, the 5 prime-most primer 307387 has the sequence CACTG..... It also has a polymorphism at the 17 nucleotide of this 25 nt probe sequence.
	How do we know that the 5 prime probe is polymorphic? By looking up the sequence in the Celera Genomics databases which often contqains sequence data for C57BL/6J (B6 above) and for DBA/2J.  But two blue probes (14 and 15) do NOT contain SNPs but still have very large LRS scores. The other probes do not perform so wel. Highly variable probe performance is probably a result of the very different stacking energies of DNA-RNA duplexes.