Using pos and extracting character positions and according actual offsets (useful to substr) it could look as outlined below. I'm not saying however, that this 'solution' is better (just another possible approach): 
use strict;
use warnings;

my @strings = do { local $/; split /\n/, <DATA> };

foreach my $str (@strings) {
    my $ret = offset($str);
    my $substring = substr($ret->[0], $ret->[2][0], $ret->[2][1]);

    print <<"EOT";
$substring
start character: $ret->[1][0]
end   character: $ret->[1][1]
start    offset: $ret->[2][0]
end      offset: $ret->[2][1]

EOT

}

sub offset {
    my $str = shift;

    my $hyphens = 0;
    $hyphens++ while $str =~ /-/g;

    $str =~ /[A-Z]/g and my $pos_start = pos($str);
    $str =~ /[a-z]/g and my $pos_end   = pos($str);

    return [ $str,
             [ ($pos_start - $hyphens), ($pos_end - $hyphens) - 1 ],
             [ $pos_start - 1, ($pos_end - $pos_start) - 1        ]
           ];
}

__DATA__
ccaatTTTGACACACACAGAAgggca
--aatTTTGACACACACAGAAgggca

[download]
outputs 
TTTGACACACACAGA
start character: 6
end   character: 21
start    offset: 5
end      offset: 15

TTTGACACACACAGA
start character: 4
end   character: 19
start    offset: 5
end      offset: 15

[download]
Update: fix formatting.

In reply to Re: Finding Start/End Position of the Uppercase Substring by shigetsu
in thread Finding Start/End Position of the Uppercase Substring by neversaint

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