Allowed options:

--allow-redundant arg (=1)

allow redundant alignments?

--chain arg (=1)

chain seeds?

--extend arg (=1)

perform gapped extension on chains?

--window arg (=-1)

size of window to use during gapped extension

--gapopen arg (=0)

gap open penalty

--gapextend arg (=0)

gap extension penalty

--h arg (=0.00800000038)

Transition to Homologous

--help

get help message

--highest arg (=procrast.highest) file containing highest scoring alignment

for each multiplicity

--l arg (=1)

minimum repeat length

--large-repeats arg (=0)

optimize for large repeats

--load-sml arg (=0)

try to load existing SML file?

--onlydirect arg (=0)

only process seed matches on same strand?

--onlyextended arg (=0)

only output extended matches?

--output arg

procrastAligner output

--percentid arg (=0)

min repeat family % id

--novel-subsets arg (=0)

find novel subset matches?

--novel-matches arg (=1)

use novel matches found during gapped extension?

--rmax arg (=500)

maximum repeat multiplicity (max copy number)

--rmin arg (=2)

minimum repeat multiplicity (min copy number)

--seeds arg

seed output file

--sequence arg

FastA sequence file

--small-repeats arg (=0)

optimize for small repeats

--score-out arg

output with corresponding score and alignment info

--solid arg (=0)

use solid/exact seeds?

--sp arg (=0)

minimum Sum-of-Pairs alignment score

--tandem arg (=1)

allow tandem repeats?

--two-hits arg (=0)

require two hits within w to trigger gapped extension?

--u arg (=0.00100000005)

Transition to Unrelated

--unalign arg (=1)

unalign non-homologous sequence?

--w arg (=0)

max gap width

--xmfa arg

XMFA format output

--xml arg

XML format output

--z arg (=0)

seed weight