Mauve returns 'gap encountered' error

[iacobo]

When attempting to run progressiveMauve, it returns the following error:

Sequence loaded successfully.ERROR! gap character encountered at genome sequence position 1732758
Input sequences must be unaligned and ungapped!

The problematic file is contigsOutput_3.fa.

Have checked file searching for regex [ACGT]- and found no results (- is the gap character).
Sarah has suggested N's might be the issue, but these appear in all other un-problematic files checked also.

Google implies it may be an EOL/Unicode issue:

https://sourceforge.net/p/mauve/mailman/message/25982371/

Possible since this is one of the files which were generated with a generic name and no file extension, and were just renamed _X.fa.