AdrianJ217:

Something like this should work:

my $s1='TCGAGTGGCCATGAACGTGCCAATTG';
my $s2='ATGATCCTG';
($s1,$s2) = ($s2,$s1) if length($s1) > length($s2);
my $loc = index $s2, $s1;
if ($loc<0) {
   print "String not found!\n";
}
else {
   print "String found at location $loc\n";
}
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