bg.order = [1] 3
cluster.rows.allowed = [1]  3 70
cmonkey.filename = [1] "cmonkey_4.1.5_hal_2072x268_09_Oct_07_11:51:17"
cmonkey.session.info =                                                             platform 
                                             i386-apple-darwin8.11.1 
                                                                arch 
                                                                i386 
                                                                  os 
                                                        darwin8.11.1 
                                                              system 
                                                  i386, darwin8.11.1 
                                                              status 
                                                                     
                                                               major 
                                                                   2 
                                                                     
                                                                 ... 
                                              loadedOnly.tools.Title 
                                       Tools for Package Development 
                                             loadedOnly.tools.Author 
                                    Kurt Hornik and Friedrich Leisch 
                                         loadedOnly.tools.Maintainer 
                                  R Core Team <R-core@r-project.org> 
                                        loadedOnly.tools.Description 
    Tools for package development, administration and\ndocumentation 
                                            loadedOnly.tools.License 
                                                     Part of R 2.9.2 
                                              loadedOnly.tools.Built 
R 2.9.2; universal-apple-darwin8.11.1; 2009-08-24 14:46:12 UTC; unix 
cmonkey.time.ended = [1] "Wed Oct  7 23:08:52 2009"
cmonkey.time.started = [1] "Wed Oct  7 11:51:17 2009"
cmonkey.version = [1] "4.1.5"
cog.org = [1] "Hbs"
date.run = [1] "09 Oct 07 11:51:17"
fuzzy.index =  [1] 0.7485014990005     0.747005992007994   0.745513473040451  
 [4] 0.744023936127795   0.742537375311876   0.741053784646448  
 [7] ...                 0.00187774803765157 0.00187399629456993
[10] 0.00187025204747597 0.00186651528139269 0.00186278598137302
[13] 0.00185906413249977
grouping.weights = numeric(0)
k.clust = [1] 200
mast.addl.args = [1] "-ev 99999 -mev 99999 -mt 0.99 -seqp -remcorr"
mast.cmd = [1] "progs/mast"
max.changes = rows cols 
 0.2  5.0 
meme.addl.args = [1] "-time 600 -maxsize 9999999 -nmotifs %1$d -evt 1e9 -minw %2$d -maxw %3$d -mod zoops"
meme.cmd = [1] "progs/meme"
meme.consensus = [1] "compute"
meme.consensus.e.val.limit = [1] 0.1
meme.seqs.allowed = [1]  3 70
merge.cutoffs =     n   cor 
0.300 0.975 
mot.iters =  [1] 100  200  300  400  500  600  ...  2500 2600 2700 2800 2900 3000
mot.scaling =  [1] 0                    0.000166777851901267 0.000333555703802535
 [4] 0.000500333555703802 0.00066711140760507  0.000833889259506338
 [7] ...                  0.249166110740494    0.249332888592395   
[10] 0.249499666444296    0.249666444296197    0.249833222148099   
[13] 0.25                
motif.palindrome.option = [1] "non"
motif.upstream.scan = [1] -30 250
motif.upstream.search = [1] -20 150
motif.width.range = [1]  6 24
n.clust.per.col = [1] 133
n.clust.per.row = [1] 2
n.iter = [1] 3000
n.motifs =  [1] 1   1   1   1   1   1   ... 2   2   2   2   2   2  
net.iters =  [1] 1    8    15   22   29   36   ...  2962 2969 2976 2983 2990 2997
net.scaling =  [1] 0                    6.6711140760507e-05  0.000133422281521014
 [4] 0.000200133422281521 0.000266844563042028 0.000333555703802535
 [7] ...                  0.0996664442961975   0.099733155436958   
[10] 0.0997998665777185   0.099866577718479    0.0999332888592395  
[13] 0.1                 
net.weights =  string operons 
    0.5     0.5 
no.genome.info = [1] FALSE
operon.shift = [1] TRUE
organism = [1] "hal"
parallel.cores = [1] TRUE
pareto.adjust.scalings = [1] TRUE
penalize.probes.without.seqs = [1] TRUE
plot.iters =  [1] 2    27   52   77   102  127  ...  2852 2877 2902 2927 2952 2977
post.adjust = [1] FALSE
remove.low.complexity.subseqs = [1] TRUE
resid.iters =  [1] 1    3    5    7    9    11   ...  2989 2991 2993 2995 2997 2999
resid.scaling =  [1] 1   1   1   1   1   1   ... 1   1   1   1   1   1  
rnd.seed = [1] 1254941477
rsat.species = [1] "Halobacterium_sp"
rsat.urls = [1] "http://rsat.ulb.ac.be/rsat/"         "http://rsat.ccb.sickkids.ca/"       
[3] "http://embnet.ccg.unam.mx/rsa-tools"
save.logfile = [1] FALSE
seed.method =           rows           cols 
"net=string:5"         "best" 
stats.iters =  [1] 1    5    10   15   20   25   ...  2975 2980 2985 2990 2995 3000
taxon.id = [1] 64091
translation.tab =           V1      V2
1   VNG5003H VNG7002
2   VNG5005H VNG7003
3   VNG5007H VNG7005
4   VNG5008H VNG7006
5   VNG5009H VNG7007
6   VNG5010G VNG7008
7       <NA>    <NA>
142 VNG5240G VNG7169
143 VNG5242G VNG7170
144 VNG5245G VNG7171
145 VNG5253H VNG7174
146 VNG5255H VNG7175
147 VNG5256H VNG7176
uniquify.seqs = [1] TRUE