$ matchcluster -gapsize 1000 -outprefix clout ychrIII-100.match
# file=/vol/biodata/DNA-mix/Grumbach.fna/ychrIII.fna 320531 315339
# databaselength=315338
# alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped to "acgtn" (size 5)
# ychrIII.fna.tis read
# ychrIII.fna.ois read
# ychrIII.fna.des read
# ychrIII.fna.sds read
# read self matches
# cluster 16 matches
# create cluster 0 of size 9
# create cluster 1 of size 4
