use warnings;
use strict;

my %hash;
my $key;

while (<DATA>) {
    next if /^\s+$/;
    if (/^>/) {
        $key = $_;
    }
    else {
        $hash{$key} = $_;
    }
}

print map { $_->[0], $hash{ $_->[0] }, $/ }
  sort { $a->[1] <=> $b->[1] }
  map { [ $_, /(\d+$)/ ] } keys %hash;

__DATA__
>or3
agagatgatagat

>or10

aacctttagtag

>or1

gtatatatata

>or2

tactacatgagg