============================================================= /tmp/gibbs9188/Gibbs9188 /tmp/gibbs9188/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/gibbs9188/prior.txt -R 1,1,8 -U /tmp/gibbs9188/spacing.txt -M 1,24 -B /tmp/gibbs9188/data.txt_info-det -y -nopt -o /tmp/gibbs9188/outfile.txt Gibbs 3.10.001 Sep 8 2009 Data file: /tmp/gibbs9188/data.txt Output file: /tmp/gibbs9188/outfile.txt Priors file: /tmp/gibbs9188/prior.txt Background Composition Model file: /tmp/gibbs9188/data.txt_info-det Spacing Model file: /tmp/gibbs9188/spacing.txt Current directory: /tmp/gibbs9188 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 = 1338376669 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: 2750 Total sequence length: 2750 ====================================================================== ======================== MAP MAXIMIZATION RESULTS ==================== ====================================================================== ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 63 . . 36 0.6 2 | 63 18 . 18 0.4 3 | 9 9 18 63 0.4 4 | 9 90 . . 0.9 5 | 72 . 27 . 0.7 6 | 45 45 . 9 0.3 7 | . 81 9 9 0.7 8 | . 9 . 90 1.1 9 | 9 18 72 . 0.7 10 | 81 . . 18 0.8 11 | 63 36 . . 0.5 12 | . 81 9 9 0.7 13 | 81 . 18 . 0.8 14 | 27 45 18 9 0.1 15 | . 54 45 . 0.6 16 | . 63 18 18 0.4 nonsite 27 29 20 22 site 32 34 14 17 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.581 0.045 0.032 0.342 2 | 0.581 0.199 0.032 0.189 3 | 0.119 0.122 0.186 0.573 4 | 0.119 0.814 0.032 0.035 5 | 0.658 0.045 0.263 0.035 6 | 0.427 0.430 0.032 0.112 7 | 0.042 0.737 0.109 0.112 8 | 0.042 0.122 0.032 0.804 9 | 0.119 0.199 0.647 0.035 10 | 0.734 0.045 0.032 0.189 11 | 0.581 0.353 0.032 0.035 12 | 0.042 0.737 0.109 0.112 13 | 0.734 0.045 0.186 0.035 14 | 0.273 0.430 0.186 0.112 15 | 0.042 0.507 0.416 0.035 16 | 0.042 0.584 0.186 0.189 Background probability model 0.270 0.290 0.211 0.229 16 columns Num Motifs: 11 2, 1 48 tagag AACTAGTGCATTAGCT tattt 63 0.90 F aroH2 5, 1 129 cgctg GAGTATTGAGATAATT ttcag 144 0.77 F aroKB1 5, 2 153 agtct GACTCTCGCAATATCT tatga 168 0.94 F aroKB1 7, 1 139 cacag GAATAATGTATTACCT gtggt 154 0.91 F aroA 8, 1 94 gctaa ATGTAATTTATTATTT acact 109 0.00 F aroL 9, 1 120 gccga AATTATTGCGATCATG ccctg 135 0.56 F aroC 10, 1 148 attgg AAGTATTGCATTCACT aagat 163 0.96 F aroG 10, 2 169 aagat AAGTATGGCAACACTG gaaca 184 0.54 F aroG 11, 1 22 cgggt GGGTAATGCAATATTC ttttc 37 0.98 F aroD+ydiB 11, 2 43 ttttc AGGTCATGCAAGATCT tacgg 58 0.94 F aroD+ydiB 11, 3 116 aaact ATGACATGCAATATTC ctgga 131 0.55 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 = -174.63130 Log Fragmentation portion of MAP for motif a = -0.00000 Log Background portion of Map = -3557.52488 Log Alignment portion of Map = -73.11557 Log Site/seq portion of Map = 0.00000 Log Null Map = -3798.83776 Non Palindromic Map = -12.93336 Log Map = -6.43399 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null Frequency Map = -7.165969 Nearopt Map = -7.165969 Maximal Map = -6.433989 Elapsed time: 23.500000 secs