=============================================================
/tmp/gibbs9268/Gibbs9268 /tmp/gibbs9268/data.txt 16 20 -E 2 -n -r -W 0.8 -w 0.1 -p 200 -j 5 -i 2000 -S 40 -C 0.5 -P /tmp/gibbs9268/prior.txt -R 1,1,8 -U /tmp/gibbs9268/spacing.txt -M 1,24 -B /tmp/gibbs9268/data.txt_info-det -y -nopt -o /tmp/gibbs9268/outfile.txt 
 
 
Gibbs 3.10.001  Sep  8 2009
Data file: /tmp/gibbs9268/data.txt
Output file: /tmp/gibbs9268/outfile.txt
Priors file: /tmp/gibbs9268/prior.txt
Background Composition Model file: /tmp/gibbs9268/data.txt_info-det
Spacing Model file: /tmp/gibbs9268/spacing.txt
Current directory: /tmp/gibbs9268
The following options are set:
Concentrated Region          False    Sequence type        False
Collapsed Alphabet           False    Pseudocount weight   True 
Use Expectation/Maximization False    Don't Xnu sequence   False
Help flag                    False    Near optimal cutoff  True 
Number of iterations         True     Don't fragment       False
Don't use map maximization   False    Repeat regions       False
Output file                  True     Informed priors file True 
Plateau periods              True     palindromic sequence True 
Don't Reverse complement     True     Number of seeds      True 
Seed Value                   False    Pseudosite weight    True 
Suboptimal sampler output    False    Overlap              False
Allow width to vary          False    Wilcoxon signed rank False
Sample along length          False    Output Scan File     False
Output prior file            False    Modular Sampler      True 
Ignore Spacing Model         False    Sample Background    False
Bkgnd Comp Model             True     Init from prior      False
Homologous Seq pairs         False    Parallel Tempering   False
Group Sampler                False    No progress info     False
Fragment from middle         False    Verify Mode          False
Alternate sample on k        False    No freq. soln.       True 
Calc. def. pseudo wt.        False    Motif/Recur smpl     False
Phylogenetic Sampling        False    Supress Near Opt.    True 
Nearopt display cutoff       False    Sample model         False
Hierarchical Model           False    Centroid model       False
Print Bayesian Counts        False    Align Centroid       False
Calculate Credibility Limits False    Frequency Bkgnd.     False
 
site_samp            =            0
nMotifLen            =           16
nAlphaLen            =            4
nNumMotifs           =           20
dPseudoCntWt         =          0.1
dPseudoSiteWt        =          0.8
nMaxIterations       =         2000
lSeedVal             =   1338379525
nPlateauPeriods      =          200
nSeeds               =           40
nNumMotifTypes       =            1
dCutoff              =          0.5
dNearOptDispCutoff   =          0.5
RevComplement        =            0
glOverlapParam       =            0
Max Sites/seq        =            2
Min Sites/Seq        =            0
Rcutoff factor       =            0
Post Plateau Samples =            0
Frag/Shft Per.       =            5
Frag width           =           24
 
 
Sequences to be Searched:
_________________________
#1   pheA
#2   aroH2
#3   tyrB
#4   aroKB1
#5   aroF+tyrA
#6   aroA
#7   aroL
#8   aroC
#9   aroG
#10  aroD+ydiB
Processed Sequence Length: 2000 Total sequence length: 2000
 
 
 
 
 
 
 
 
 
 
======================================================================
======================== MAP MAXIMIZATION RESULTS ====================
======================================================================
 
-------------------------------------------------------------------------
                          MOTIF a
 
               No Motifs Detected
 
 
Log Background portion of Map = -2756.69396
Log Alignment portion of Map = 0.00000
Log Site/seq portion of Map = -4.82487
Log Null Map = -2761.51883
Non Palindromic Map = -0.00000
Log Map = -0.00000
 
 
log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null
 
Frequency Map = -0.000000
Nearopt Map   = -0.000000
Maximal Map   = -0.000000
Elapsed time: 15.340000 secs