How could I see with gnuplot my target and template graphics in the same
window, as appear in the tutorial.
You probably don't want to do that in most cases, because the DOPE
energy for target and template is not quantitatively comparable. But if
you really want to do it, you'll have to correct for gaps. The
"plotdope" script in the wiki may be of use to you:
http://salilab.org/modeller/wiki/Plotdope