Here's another approach. In addition to collecting user input, it tries to control (the user can exit the collection loop early using loop control) and validate (using regexes or regular expressions — see perlre, perlretut, perlreref and perlrequick for info on these) the input. Any upper- or lower-case alpha character is accepted as a "DNA" character, but you can alter the validation regex to refine this for your application. It also has some debug statements; take them out for final use. :)

Script: get_seqs_1.pl:

use strict;
use warnings;

use Data::Dumper;  # for debug

use constant {  # regexes to check and control input
    BLANK_LINE => qr{ \A \s* \Z }xms,
    NON_SEQ    => qr{ [^[:alpha:]] }xms,  # could be ATCG or IUPAC
    };

use constant USER_PROMPTS_IN_ORDER => qw(first secundus third 4th);

my %prompted_seqs;  # collected info on prompted sequences entered by 
+user

print "please enter DNA sequences: \n";
PROMPT:
for my $prompt (USER_PROMPTS_IN_ORDER) {
    print "  $prompt sequence: ";
    my $input = <STDIN>;
    chomp $input;
    print("  stop getting sequences: user request \n"), last PROMPT
        if $input =~ BLANK_LINE;
    print("  stop getting sequences: bad input: '$input' \n"), last PR
+OMPT
        if $input =~ NON_SEQ;
    $prompted_seqs{$prompt}{seq} = $input;
    $prompted_seqs{$prompt}{len} = length $input;
    }

print Dumper \%prompted_seqs;  # for debug

print "valid entered sequences in order of prompt: \n";
print "  $_: $prompted_seqs{$_}{seq} ($prompted_seqs{$_}{len}) \n"
    for grep { exists $prompted_seqs{$_} } USER_PROMPTS_IN_ORDER;

print "valid entered sequences in order of increasing length: \n";
print "  $_: $prompted_seqs{$_}{seq} ($prompted_seqs{$_}{len}) \n"
    for sort { $prompted_seqs{$a}{len} <=> $prompted_seqs{$b}{len} }
        keys %prompted_seqs
        ;
[download]

Win8 Strawberry 5.8.9.5 (32)  Sun 09/20/2020 22:47:03
C:\@Work\Perl\monks\shabird
>perl get_seqs_1.pl
please enter DNA sequences:
  first sequence: dddddd
  secundus sequence: sss
  third sequence: ffffffffff
  4th sequence: gggggg
$VAR1 = {
          'first' => {
                       'len' => 6,
                       'seq' => 'dddddd'
                     },
          'secundus' => {
                          'len' => 3,
                          'seq' => 'sss'
                        },
          '4th' => {
                     'len' => 6,
                     'seq' => 'gggggg'
                   },
          'third' => {
                       'len' => 10,
                       'seq' => 'ffffffffff'
                     }
        };
valid entered sequences in order of prompt:
  first: dddddd (6)
  secundus: sss (3)
  third: ffffffffff (10)
  4th: gggggg (6)
valid entered sequences in order of increasing length:
  secundus: sss (3)
  first: dddddd (6)
  4th: gggggg (6)
  third: ffffffffff (10)
[download]