##################################################################
# msatfinder.rc - configuration file for msatfinder script only. #
# Full editing instructions are included below.							     # 
# most of these defaults should be acceptable. 									 #
##################################################################


[COMMON]

# set to 1 to switch on debugging info
debug = 0

# no. of bp either side of each msat to extract
flank_size = 300

# directory variables: it is best to leave these
# values as they are. If you change them, the trailing
# slash MUST be left on the name
mine_dir = "MINE/"
repeat_dir = "Repeats/"
tab_dir = "Msat_tabs/"
bigtab_dir = "Flank_tabs/"
fasta_dir = "Fasta/"
prime_dir = "Primers/"
align_dir = "Aligner/"
count_dir = "Counts/"


[DEPENDENCIES]

# Determine whether primers may be made from the repeat  you need eprimer3 
# (emboss),  and primer3_core on your PATH for this to work				   
# (see http://www-genome.wi.mit.edu/genome_software/other/primer3.html)	   
# see eprimer3 documentation for additional flags.						   	
# N.B. use "-task 0" if you have EMBOSS v.2.8.0, but "-primer" if you
# have a newer version.
run_eprimer = 1
eprimer_args = "-primer"
eprimer = "/usr/bin/eprimer3"
primer3core = "/usr/bin/primer3_core"

# full paths to various executables 
# check that these are correct for 
# your system before running        
bl2seq = "/usr/bin/bl2seq"
bl2seq_options = "-F F"
blast_type = "blastn"

[FINDER]

# the override switch will, if set to 1, 
# turn off most of the output files.     
# they can be deactivated individually   
# with separate switches (see below)     
override = 0

# set the thresholds here, in order: 
# mono, di, tri, tetra, penta, hexa... &c. 
# msatfinder will find msats of that
# no. of units or more
threshold = "12,8,5,5,5,5"

# set the type of msat you want to search
# for here, 1=mono, 2=di etc. Default is
# for mono-hexa
mrange="1,2,3,4,5,6"

# will write a file.tab file for you      
# with repeats formatted as embl features 
# ready for overlay on the genbank doc    
# inside the artemis annotation tool      
# contains "feature table", hence "tab" 
# 0 no artemis files 
# 1 files for msat only
# 2 also produce separate files for msat + flanks
artemis = 1

# Write repeats and flanking areas to 
# a MINE.db file? 1=yes, etc.         
mine = 1

# write fasta files for repeats? 
fastafile = 1

# "taxon" information: please see					  
# http://genomics.nerc-oxford.ac.uk/msatminer/#taxon  
# for details										  
phages = "viruses"
viroids = "viruses"
plant_viruses = "viruses"
megaplasmids = "plasmids"

# remote link for viewing complete 
# files, (Genbank, in this case)   
remote_link="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="

# this switch turns on the Repeats/$prefix.summary 
# file, which can grow rather large if your        
# thresholds are low. It's an essential file, though.                             
sumswitch = 1

# print out filenames as they are searched 
screendump = 1