my @seq_data;
open(SEQ,'<',$sequence_fname)||die "Cannot open sequence file\n";
while (<SEQ>) {
    push @seq_data, [split /\t/];
}
close SEQ;

if(!($permute)){
    for (@seq_data) {
        my @line = @$_;
        ...
    }
    ...
{
else{
    open(OUT,">>$out")||die "Cannot open $out\n";

    for (...) {
        ...
        for (@seq_data) {
            my @line = @$_;
            ...
        }

        foreach my $key(keys %ktc){
            ...
            print OUT ...
            ...
        }
    }

    close OUT;
}