my $newline = 
  "TTTATGCACTCATGTTTAGACATATTTCCTACACCCATATTTGAAGACCA\r"
. "... other lines (overprinted) ...\r"
. "TAGATTCTGTAAACTGTGTCCATTTCTGTGCCTATTTACTTGGTATTTGT\r"
. "TAACTCTTAGTACACATAAGTTTACGTACC\r";

print "\$newline is: $newline\n";  # (this is your debug print)