open(IN1, '<', $input1) or die "Can't read source file $input1 : $!\n";
my $minlength = 1<<20;
my %distrbtn;

while(<IN1>) {
    next if />/;
    chomp;
    my $len = length();
    $distrbtn{$len}++;
    $minlength = $len if ( $minlength > $len );
}
close IN1;
$minlength -= 3;

open(IN2, '<', $input2) or die "Can't read source file $input2 : $!\n";
my $header;
my @source;
my %source_lengths;

while(<IN2>) {
    chomp;
    if ( />/ ) {
        $header = $_;
    }
    elsif ( length() >= $minlength ) {
        push @source, $header;
        push @source, $_;
        push @{$source_lengths{length()}}, $#source;
    }
}
close IN2;