 in second sequence (A_j_&lt;sequence_id&gt;)</span>
<span class="sd">    &quot;&quot;&quot;</span>
    <span class="c1"># read alignment that is basis of mapping</span>
    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">alignment_file</span><span class="p">)</span> <span class="k">as</span> <span class="n">a</span><span class="p">:</span>
        <span class="n">ali</span> <span class="o">=</span> <span class="n">Alignment</span><span class="o">.</span><span