use strict;
use warnings;

my %sequence;

while (my $seq = <DATA>) {
  if ($seq =~ /^(\w+)\s*=>\s*(\d+)/) {
    $sequence{$1} = $2 unless defined $sequence{$1} && $sequence{$1} >
+ $2;
  }
}
for my $key (sort keys %sequence) {
  print "$key $sequence{$key}\n";
}

__DATA__
CIMG_00046 => 399
CIMG_00047 => 865
CIMG_00048 => 330
CIMG_00048 => 506
CIMG_00053 => 167
CIMG_00063 => 468
CIMG_00063 => 467
CIMG_00063 => 466
CIMG_00063 => 469
CIMG_00063 => 460
__END__

CIMG_00046 399
CIMG_00047 865
CIMG_00048 506
CIMG_00053 167
CIMG_00063 469
[download]

Hashes cannot have multiple same-named keys at the same level.

perl -le '
use Data::Dump qw/dump/;
%hash = {
  a => 3,
  a => 2,
  a => 1,
  b => 6,
};
print dump \%hash;
'
{ a => 1, b => 6 }
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