Still not a lot of info to do | go on, but let me suggest you have "invisible" characters lurking in your input: 

c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le
"my $seq = qq{what is wrong with this\x0dline};
 print $seq;
 dd $seq;
"
line is wrong with this
"what is wrong with this\rline"

[download]
Some kind of data dump (Data::Dumper, Data::Dump) might be informative. (Data::Dumper is core and so should already be installed.)

Give a man a fish:  <%-{-{-{-<

In reply to Re^3: missing character when reading input file by AnomalousMonk
in thread missing character when reading input file by JediGorf

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