probe.pl < probe_input.file > output.file

##</code><code>##

#! C:\Perl\bin\perl

use strict;
use warnings;

my $target_name = '';
my %probes;

while (<>) {
    if ( /:(\d{6})_/ ) {  #this line has a target name
        if ( $target_name ne $1 ) {
            $target_name = $1;
            print STDERR "$target_name\n";
        }
    }
    if ( /\b([ACGT]{20})/ ) { # this line has a probe string
        my $probe = $1;
        print STDERR "$probe\n";
        push @{$probes{$target_name}}, $probe;
    }
}

# printing to STDOUT with redirection on the command line
# will save results in an output file (whereas printing to
# STDERR goes to the shell window -- unless you use a bash
# or bourne-style shell, which allows you to redirect
# STDERR to a separate file, using "2> errlog.file")

for (sort{ @{$probes{$b}} <=> @{$probes{$a}} } keys %probes) {
    print "$_, ", join(", ", sort @{$probes{$_}}), "\n";
}