umns:
##       queryHits subjectHits
##       &lt;integer&gt;   &lt;integer&gt;
##   [1]         2           1
##   [2]         2           2
##   [3]         2           3
##   [4]         2           4
##   -------
##   queryLength: 2 / subjectLength: 4</code></pre>
<p>Note how the <code>queryLength</code> is 2 and not 20. What we know from the first row of this output is that some range in <code>gL[[2]]</code> overlaps the range <code>gr[1]</code>.</p>
<p>This is actually a feature if we think of the <co