use strict;
use warnings;

open my $reg_out  , '>', 'RegularOligos.txt'   or die "can not open file RegularOligos.txt:$!";
open my $irreg_out, '>', 'IrregularOligos.txt' or die "can not open file IrregularOligos.txt:$!";
while(<DATA>){
    chomp;
    my @fields = split;
    my $line = join "\t", @fields;
    if ($fields[0] =~ /-/){
        print $reg_out "$line\n";
    }
    else{
        print $irreg_out "$line\n";
    }
}
close $irreg_out;
close $reg_out;

__DATA__
10002TU    AGACATTACCTGTGAGACACCTTTC   GCCTCCACCTCAGAGTCAG    TCCATGGGAAGGATCTCCGTGAAATCA
10002TU-2    GCTCCAGCTAGAAGAGAATCC    CCCACCAGGGCTGTGTAAG    CCTGTGAGATAGTACAGCTGAAGAGTTGGC
10002TD    TGTGTTGATTCTCAGCCTCTTG    GACGGAGCACATAGGCAAAG    TCTGTTCTTCTCAGCTGTCTTTGTTGCTGC
10003TU    CAGCAAGCCCTGAGGTGTG    CAGTGAACTGAGAAAGACGAGAGG TGCAAGTCCAGATGGAGGCCACC
10174TU-2    ACCTGAACAGCCTGACATGAAC   TGGGATGGAGGGCAAAGTC    CCACCTAGTATGACCCAGCACACCTCC