Mysqlimport very slow when importing two smaller files
I am thinking of two things to try. If you get faster execution time, then the slowness would be related to the distribution of the data. If you still get slow execution time, it maybe then related to the server configs. 


Try to load allelePiecesab file before. If this is slow, then the data in this file has higher cardinality of key fields.
Try to disable the indexes (as this is MyIsam), and load the files in whichever order, then re-enable the keys. If this is faster, then the slowness is related to the updating time of index files after certain growth:


ALTER TABLE allele DISABLE KEYS;
// Do the load
ALTER TABLE allele ENABLE KEYS;