_score_cutoff</a>,
<a name="l00298"></a>00298            A_fine_tune_tier2_alignments, dset_site);
<a name="l00299"></a>00299     }
<a name="l00300"></a>00300 
<a name="l00301"></a>00301     <span class="comment">// If we wanted only to fine tune the best scoring alignment at this level,</span>
<a name="l00302"></a>00302     <span class="comment">// do it here</span>
<a name="l00303"></a>00303     <span class="keywordflow">if</span>(top_aligns-&gt;size() &amp;&amp; A_fine_tune_best_tier2_alignment)
<a name=