$ ramaco -v -phase output -l 6 -rare 5 ATS ATs-01 ATs-02 ATs-03
# file=ATs-00 350 275
# databaselength=274
# alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped to "acgtn" (size 5)
# ATS.tis read
# ATS.suf read
# ATS.lcp read
# searchlength = 6
# width0 = 5
# width1 = 5
# width2 = 5
# width3 = 5
# queryfile=ATs-01 of length 852
# input match file for query ATs-01 and index ATS
# queryfile=ATs-02 of length 719
# input match file for query ATs-02 and index ATS
# merge matches for queries ATs-01 and ATs-02
# common intervals=15
# queryfile=ATs-03 of length 746
# input match file for query ATs-03 and index ATS
# merge matches for query ATs-03 with previous matches
# common intervals=2
# output the matches
6 250 338 583 292
6 62 453 74 461
6 62 453 74 2
# number of rare MEMs is 3
# overall space peak: main: 0.06 MB, secondary: 0.00 MB
