n">ali</span><span class="o">.</span><span class="n">ids</span><span class="p">[</span><span class="n">target_seq_index</span><span class="p">]</span>
    <span class="p">)</span>
    <span class="n">target_seq</span> <span class="o">=</span> <span class="n">ali</span><span class="o">.</span><span class="n">matrix</span><span class="p">[</span><span class="n">target_seq_index</span><span class="p">]</span>

    <span class="c1"># now map from target numbering to hit numbering</span>
    <span class="n">full