change default max_seq_size in last alignment iteration from 1000000 to 5000000 (to avoid cactus_check failures). 
change default max_seq_size in last alignment iteration from 1000000
to 5000000 (to avoid cactus_check failures). 

Change-Id: I99d2369e354911d2a6b2961e087a3cfc6425600b

benedictpaten/cactus,benedictpaten/cactus,benedictpaten/cactus,benedictpaten/cactus,benedictpaten/cactus