============================================================= /tmp/gibbs9135/Gibbs9135 /tmp/gibbs9135/data.txt 16 20 -n -r -W 0.8 -w 0.1 -p 200 -j 5 -i 2000 -S 40 -C 0.5 -P /tmp/gibbs9135/prior.txt -R 1,1,8 -U /tmp/gibbs9135/spacing.txt -M 1,24 -B /tmp/gibbs9135/data.txt_info-det -y -nopt -o /tmp/gibbs9135/outfile.txt Gibbs 3.10.001 Sep 8 2009 Data file: /tmp/gibbs9135/data.txt Output file: /tmp/gibbs9135/outfile.txt Priors file: /tmp/gibbs9135/prior.txt Background Composition Model file: /tmp/gibbs9135/data.txt_info-det Spacing Model file: /tmp/gibbs9135/spacing.txt Current directory: /tmp/gibbs9135 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 False 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 = 1338374657 nPlateauPeriods = 200 nSeeds = 40 nNumMotifTypes = 1 dCutoff = 0.5 dNearOptDispCutoff = 0.5 RevComplement = 0 glOverlapParam = 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 aroKB2 #5 aroKB1 #6 aroF+tyrA #7 aroA #8 aroL #9 aroC #10 aroG #11 aroD+ydiB Processed Sequence Length: 2200 Total sequence length: 2200 ====================================================================== ======================== MAP MAXIMIZATION RESULTS ==================== ====================================================================== ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 71 . 28 . 0.6 2 | 42 . 28 28 0.2 3 | 71 28 . . 0.5 4 | 14 . . 85 0.8 5 | 14 . 42 42 0.4 6 | 85 . . 14 0.7 7 | 42 14 14 28 0.1 8 | . 100 . . 0.9 9 | 100 . . . 1.0 10 | 42 28 . 28 0.2 11 | . 100 . . 0.9 12 | . . 57 42 0.6 13 | . 42 57 . 0.5 14 | 28 57 . 14 0.2 15 | . 85 . 14 0.7 16 | . 85 . 14 0.7 nonsite 26 29 20 22 site 32 33 14 19 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.615 0.065 0.269 0.051 2 | 0.393 0.065 0.269 0.273 3 | 0.615 0.288 0.046 0.051 4 | 0.171 0.065 0.046 0.718 5 | 0.171 0.065 0.380 0.384 6 | 0.726 0.065 0.046 0.162 7 | 0.393 0.177 0.157 0.273 8 | 0.059 0.843 0.046 0.051 9 | 0.837 0.065 0.046 0.051 10 | 0.393 0.288 0.046 0.273 11 | 0.059 0.843 0.046 0.051 12 | 0.059 0.065 0.491 0.384 13 | 0.059 0.399 0.491 0.051 14 | 0.282 0.510 0.046 0.162 15 | 0.059 0.732 0.046 0.162 16 | 0.059 0.732 0.046 0.162 Background probability model 0.264 0.292 0.212 0.231 16 columns Num Motifs: 7 1, 1 108 gttga AGAAGAGTAGTCCTTT atatt 123 0.63 F pheA 2, 1 94 gtact AGAGAACTAGTGCATT agctt 109 0.60 F aroH2 4, 1 125 ccgta AAAGCGGTAATGTTTT tacgc 140 0.69 F aroKB2 7, 1 185 tagcc ACAGGAATAATGTATT 200 0.77 F aroA 10, 1 134 taatt CCAGGATTAATCCGTT catag 149 0.74 F aroG 11, 1 76 tgggt AATGCAATATTCTTTT caggt 91 0.79 F aroD+ydiB 11, 2 170 tatga CATGCAATATTCCTGG aaaca 185 0.74 F aroD+ydiB **************** Column 1 : Sequence Number, Site Number Column 2 : Left End Location Column 4 : Motif Element Column 6 : Right End Location Column 7 : Probability of Element Column 8 : Forward Motif (F) or Reverse Complement (R) Column 9 : Sequence Description from Fast A input Log Motif portion of MAP for motif a = -111.01453 Log Fragmentation portion of MAP for motif a = -0.00000 Log Background portion of Map = -2890.25793 Log Alignment portion of Map = -51.53751 Log Site/seq portion of Map = 0.00000 Log Null Map = -3044.34747 Non Palindromic Map = -16.04418 Log Map = -8.46250 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null Frequency Map = -8.462502 Nearopt Map = -8.462502 Maximal Map = -8.462502 Elapsed time: 16.470000 secs