use strict;
use warnings;
use feature qw(:5.14);

my $line_out = <DATA>;
chomp $line_out;
while (<DATA>) {
	chomp;
	if ($_=~/^> ([\d\.\-]+)/) {
		$line_out .= $1;
	} else {
		say $line_out;
		$line_out = $_;
	}
}
say $line_out;


__DATA__
.06669701$-.1672469$.02157899$.0346167$.65879324$.91614802$.45012441$rs11080516
[... I have abbreviated your data for this post ...]