Using your convention of the first letter in the string being 1, rather than the Perl way of 0. if you want to do anything in Perl with theses numbers you need to subtract one from both the start and end offsets.

#                         1         2         3
#                123456789012345678901234567890
my $str_type1 = "ccaatTTTGACACACACAGAAgggca"; # no dash
my $str_type2 = "--aatTTTGACACACACAGAAgggca"; # with dash

for ( $str_type1, $str_type2 )
{
    if ( m{^(-*)[^A-Z]*([A-Z]*)} )
    {
        my ( $s, $e ) = ( $-[2] + 1, $+[2] );
        $_ -= length $1 for $s, $e;
        print "$_\n";
        print "From = $s to $e\n\n";
    }
}
#output:
ccaatTTTGACACACACAGAAgggca
From = 6 to 21

--aatTTTGACACACACAGAAgggca
From = 4 to 19
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