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PEGYNDRQAVNGSFYKLTFAPTFKVGSIGDFFSRPEIRFYTSWMDWSKKLNNYA
......................................................

while ($rest=~/\<REGION seq\_beg\=\"(\d+)\"\s+pdb\_beg\=\"\d+\"\s+seq\
+_end\=\"(\d+)\"\s+pdb\_end\=\"\d+\"\s+type\=\"(\w+)\"\/\>/mg)
{
...
        substr($topo_initial, ($start-1), ($end-$start+1), ('U' x ($en
+d-$start+1)));
    }
}

413     1-6
413     7-15
...
413     348-355
413     356-369
substr outside of string at myscript.pl