As documented in How do I post a question effectively?, please enclose your code in <code> tags so that people can read it:

<code>
... your code here ...
</code>

Here's your code run through Perl::Tidy so that anyone else can help more easily:

use warnings;

print "Please enter the cns file:\n";
chomp($t = <STDIN>);

open(THE, $t) or die "Can not open file: $!\n";
@data = <THE>;
close THE;

$sequence = '';
$end      = 0;

foreach $line (@data) {
    if ($line =~ /^\@/) {
        $chro = $line;
    } elsif ($line =~ /^[a-zA-Z]/) {
        $sequence .= $line;
    } else {
        $end++
    }
}

$sequence =~ s/\s*$//g;

print $chro,     "\n";
print $sequence, "\n";
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