#!/usr/bin/perl

use strict;
use warnings;
use Tie::File;

my $file = 'BlastOutput.txt';
my %hash;
my $i = 1;

tie my @array,'Tie::File',$file or die $!;
chomp @array;
while($i < scalar(@array)-1){
   push(@{$hash{$array[$i]}},$array[$i+1]);
   $i += 2;
}
untie @array;

open(my $fh,$file) or die $!;
for my $key(keys(%hash)){
  print $fh $key,"\n",join("\n",@{$hash{$key}}),"\n";
}
close $fh;