^M is vi's representation of carriage returns. When you prit them in Perl, it causes the cursor to move to the beginning of the line. For example, try

# \015 is carriage return.
print("Hello\015you\n");
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You should see "youlo" on the screen. If you redirect the above to a file and open it in vi, you will see "Hello^Myou".

The following Perl code will remove CRs:

while (<>) {
   s/\015//g;
   print $_;
}
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