Hello nica,

If you look carefully at this line:

print OUT "Genome: \n $line\n";
#                  ^^      ^^
[download]

you will see that you are adding the newlines yourself! Here is one approach that does what you want:

use strict;
use warnings;

print 'Genome: ';

while (my $line = <DATA>) 
{
    $line =~ s/^[0-9]+//;   # Remove initial digits
    $line =~ s/\s+//g;      # Remove all whitespace (including newline
+s)

    print $line if $line =~ /[acgt]+/;
}

print "\n";

__DATA__
INPUT

ORIGIN

1 ccctaaaccc taaaccctaa accctaaacc ctaaacccta aaccctaaac cctaaaccct

61 aaaccctaaa ccctaaaccc taaaccctaa accctaaacc ctaaacccta aaccctaaac

121 cctaaaccct aaaccctaaa cgatgcatta ctactcacac gaacgagtga atgaaacaca
[download]

Output:

18:35 >perl 2007_SoPW.pl
Genome: ccctaaaccctaaaccctaaaccctaaaccctaaaccctaaaccctaaaccctaaaccctaa
+accctaaaccctaaaccctaaaccctaaaccctaaaccctaaaccctaaaccctaaaccctaaacccta
+aaccctaaacgatgcattactactcacacgaacgagtgaatgaaacaca

18:35 >
[download]

Hope that helps,