# Sequel Pro doesn't actually use mysqldump, both so that it can use the
# current connection and report progress - so I can't give you the flags
# to replicate the behaviour exactly!
# However, based only on the big difference in the sizes of the files
# (and assuming you're using 0.9.3), I would bet your discrepancies/
# errors are in areas using data from TEXT/BLOB (or spatial) fields; if
#so, the option you're looking for is --hex-blob .
mysqldump -uUSERNAME -pPassword --hex-blob DATABASENAME > file.sql