use strict;
use warnings;

"ctaacxxxxxxxxxxxxxxxxxxxxxxx" =~ 
/
( #begin $1
	ct
	(a|g) # $2
	a
	(c|t) # $3
) #end $1
(.{20,50})$ # $4
/ix;

print "\n$1,$2,$3,$4";
my ($branch,$pyrich)=($1,$4);
print "\n$branch$pyrich";