an>

        <span class="c1"># adjust position in sequences if we saw a residue</span>
        <span class="k">if</span> <span class="n">res_i</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">gaps</span><span class="p">:</span>
            <span class="n">pos_i</span> <span class="o">+=</span> <span class="mi">1</span>

        <span class="k">if</span> <span class="n">res_j</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">gaps</span><span class="p"