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style='font-size:233%;color:#E9EB5D'><i>Hars2 probe level analysis: 16 PMs
mapped</i></span></div>
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mso-text-raise:0%'><span style='font-size:117%;color:#FF0F0F'><i>SNP</i></span></div>
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mso-text-raise:0%;mso-line-spacing:"100 50 0";mso-line-spacing:"100 50 0"'><span
style='font-size:117%;color:#FF0F0F'>C in B6, T in D2 </span><span
style='font-size:150%;color:black;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
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4'><i>no SNPs</i></span></div>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Let�s look at Hars2 in
more detail by mapping all of the perfect match probes (16 of them) that
target this transcript.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>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.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>You will get the
illustration above, but without the sequence data that we have added.<span
style="mso-spacerun: yes"> </span>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.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>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.<span style="mso-spacerun: yes"> </span>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.</font><br>
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