use strict;
use warnings;

my %hash;
while (<DATA>) {
    if (/>([\w]+) /) { }
    else { chomp; $hash{$1} .= $_; }
}
for (sort keys %hash) {
    print "$_ => $hash{$_}\n";
}

__DATA__
>EP11110 (-) 
TGCAATCACTAGCAAGCTCTC
GCTGCCGTCACTAGCCTGTGG
>EP40005 (+) 
GGGGCTAGGGTTAGTTCTGGA
NNNNNNNNNNNNNNNNNNNNN