the program i have written is

open(FH,"input.txt") or die "cant open";
@array=<FH>;
foreach(@array){
if($_!=~m/^>/)
{
$_=~s/\n//g;
print "$_\n";
}
}
[download]

the desired result is

#PLOT1
a b c d f g i a c g s h b h f d 
#PLOT2
b g d i s e w d u b a o n i o p w q c u s t r r y
#PLOT3
e r t d v g v g b
[download]