use strict;
use warnings;
my $filename = 'input.txt';
open (my $IN, '<', $filename) or die "Can't open file $filename : $! ";
my $text; # no need to initialize it to the empty string!
while($line = <$IN>) {
   chomp $line;  ## <---- !!!
   $text .= $line;
}
while($text =~ m/TATAAT[ACGT]+?(ATG[ACGT]+?(?:TGA|TAG|TAA))/g) {
   print "$1\n";
}