Gibbs.linux phoP_footprint.fa 14 -n -I 1,1,7 -M 1,20 -o phoP_footprint.out Gibbs 3.01.002 Feb 19 2007 Data file: phoP_footprint.fa Output file: phoP_footprint.out Current directory: /home/leeann/Gibbs_tests The following options are set: Concentrated Region False Sequence type False Collapsed Alphabet False Pseudocount weight False Use Expectation/Maximization False Don't Xnu sequence False Help flag False Near optimal cutoff False Number of iterations False Don't fragment False Don't use map maximization False Repeat regions True Output file True Informed priors file False Plateau periods False palindromic sequence True Don't Reverse complement False Number of seeds False Seed Value False Pseudosite weight False 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 False 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. False Calc. def. pseudo wt. False Motif/Recur smpl False Phylogenetic Sampling False Supress Near Opt. False Nearopt display cutoff False Sample model False Hierarchical Model False Centroid model False Print Bayesian Counts False Align Centroid False site_samp = 1 nMotifLen = 14 nAlphaLen = 4 nNumMotifs = 7 dPseudoCntWt = 0.1 dPseudoSiteWt = 0.8 nMaxIterations = 500 lSeedVal = 1178125083 nPlateauPeriods = 20 nSeeds = 10 nNumMotifTypes = 1 dCutoff = 0.01 dNearOptDispCutoff = 0.5 RevComplement = 1 glOverlapParam = 0 Rcutoff factor = 0 Post Plateau Samples = 0 Frag/Shft Per. = 5 Frag width = 20 Sequences to be Searched: _________________________ #1 mgrB genome_pos=1906820-1906867 reference=PMID: 12813061 #2 mgtA genome_pos=4465334-4465382 reference=PMID: 12123454 & PMID: 12813061 #3 phoP genome_pos=1189721-1189770 reference=PMID: 12813061 #4 rstA genome_pos=1680092-1680137 reference=PMID: 12813061 #5 slyB genome_pos=1717746-1717796 reference=PMID: 12813061 #6 vboR genome_pos=578153-578200 reference=PMID: 12813061 #7 yrbL genome_pos=3346390-3346433 reference=PMID: 12813061 Processed Sequence Length: 336 Total sequence length: 336 ====================================================================== ======================== NEAR OPTIMAL RESULTS ======================== ====================================================================== MAP = 35 maybe = 40 discard = 296 ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 14 85 . . 0.6 2 | . 71 . 28 0.5 3 | 14 . . 85 1.1 4 | . 85 . 14 0.6 5 | . 100 . . 1.0 6 | . 100 . . 1.0 7 | 100 . . . 1.4 12 | 14 57 28 . 0.5 13 | . 57 . 42 0.5 14 | 14 . . 85 1.1 15 | . 100 . . 1.0 16 | . 100 . . 1.0 17 | . 71 . 28 0.5 18 | 100 . . . 1.4 nonsite 28 38 9 23 site 18 59 2 20 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.160 0.810 0.011 0.020 2 | 0.030 0.680 0.011 0.279 3 | 0.160 0.031 0.011 0.799 4 | 0.030 0.810 0.011 0.150 5 | 0.030 0.940 0.011 0.020 6 | 0.030 0.940 0.011 0.020 7 | 0.939 0.031 0.011 0.020 12 | 0.160 0.550 0.270 0.020 13 | 0.030 0.550 0.011 0.409 14 | 0.160 0.031 0.011 0.799 15 | 0.030 0.940 0.011 0.020 16 | 0.030 0.940 0.011 0.020 17 | 0.030 0.680 0.011 0.279 18 | 0.939 0.031 0.011 0.020 Background probability model 0.324 0.298 0.130 0.248 14 columns Num Motifs: 7 1, 1 39 tcgac ATAGTTAGGCGCTGTTTA actaa 22 0.99 R mgrB genome_pos=1906820-1906867 reference=PMID: 12 2, 1 10 aagtc TGGTTTATCGTTGGTTTA gttgt 27 1.00 F mgtA genome_pos=4465334-4465382 reference=PMID: 12 3, 1 28 cccgc TGGTTTATTTAATGTTTA ccccc 11 1.00 R phoP genome_pos=1189721-1189770 reference=PMID: 12 4, 1 18 aaaac TTGTTTAGAAACGATTGA tagta 35 1.00 F rstA genome_pos=1680092-1680137 reference=PMID: 12 5, 1 14 atgtt TTGTTTATAATTGGTTGA tccta 31 1.00 F slyB genome_pos=1717746-1717796 reference=PMID: 12 6, 1 34 actca TTGTTTAGGGTTTGTTTA atttt 17 1.00 R vboR genome_pos=578153-578200 reference=PMID: 1281 7, 1 17 aggca TTGTTTAGGTTTTGTTTA agtta 34 1.00 F yrbL genome_pos=3346390-3346433 reference=PMID: 12 ******* ******* 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 = -60.44568 Log Fragmentation portion of MAP for motif a = -3.33220 ============================================================= ====== ELEMENTS OCCURRING GREATER THAN 50% OF THE TIME ===== ====== Motif a ===== ============================================================= Listing of those elements occurring greater than 50% of the time in near optimal sampling using 500 iterations Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 14 85 . . 0.6 2 | . 71 . 28 0.5 3 | 14 . . 85 1.1 4 | . 85 . 14 0.6 5 | . 100 . . 1.0 6 | . 100 . . 1.0 7 | 100 . . . 1.4 12 | 14 57 28 . 0.5 13 | . 57 . 42 0.5 14 | 14 . . 85 1.1 15 | . 100 . . 1.0 16 | . 100 . . 1.0 17 | . 71 . 28 0.5 18 | 100 . . . 1.4 nonsite 28 38 9 23 site 18 59 2 20 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.160 0.810 0.011 0.020 2 | 0.030 0.680 0.011 0.279 3 | 0.160 0.031 0.011 0.799 4 | 0.030 0.810 0.011 0.150 5 | 0.030 0.940 0.011 0.020 6 | 0.030 0.940 0.011 0.020 7 | 0.939 0.031 0.011 0.020 12 | 0.160 0.550 0.270 0.020 13 | 0.030 0.550 0.011 0.409 14 | 0.160 0.031 0.011 0.799 15 | 0.030 0.940 0.011 0.020 16 | 0.030 0.940 0.011 0.020 17 | 0.030 0.680 0.011 0.279 18 | 0.939 0.031 0.011 0.020 Background probability model 0.324 0.298 0.130 0.248 14 columns Num Motifs: 7 1, 1 39 tcgac ATAGTTAGGCGCTGTTTA actaa 22 1.00 R mgrB genome_pos=1906820-1906867 reference=PMID: 12 2, 1 10 aagtc TGGTTTATCGTTGGTTTA gttgt 27 1.00 F mgtA genome_pos=4465334-4465382 reference=PMID: 12 3, 1 28 cccgc TGGTTTATTTAATGTTTA ccccc 11 1.00 R phoP genome_pos=1189721-1189770 reference=PMID: 12 4, 1 18 aaaac TTGTTTAGAAACGATTGA tagta 35 0.65 F rstA genome_pos=1680092-1680137 reference=PMID: 12 5, 1 14 atgtt TTGTTTATAATTGGTTGA tccta 31 1.00 F slyB genome_pos=1717746-1717796 reference=PMID: 12 6, 1 34 actca TTGTTTAGGGTTTGTTTA atttt 17 1.00 R vboR genome_pos=578153-578200 reference=PMID: 1281 7, 1 17 aggca TTGTTTAGGTTTTGTTTA agtta 34 1.00 F yrbL genome_pos=3346390-3346433 reference=PMID: 12 ******* ******* Log Background portion of Map = -328.47960 Log Alignment portion of Map = -31.89864 Log Site/seq portion of Map = 0.00000 Log Null Map = -452.20576 Non Palindromic Map = 16.37105 Log Map = 28.04964 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null ====================================================================== ======================== MAP MAXIMIZATION RESULTS ==================== ====================================================================== ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 14 85 . . 0.6 2 | . 71 . 28 0.5 3 | 14 . . 85 1.1 4 | . 85 . 14 0.6 5 | . 100 . . 1.0 6 | . 100 . . 1.0 7 | 100 . . . 1.4 12 | 14 57 28 . 0.5 13 | . 57 . 42 0.5 14 | 14 . . 85 1.1 15 | . 100 . . 1.0 16 | . 100 . . 1.0 17 | . 71 . 28 0.5 18 | 100 . . . 1.4 nonsite 28 38 9 23 site 18 59 2 20 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.160 0.810 0.011 0.020 2 | 0.030 0.680 0.011 0.279 3 | 0.160 0.031 0.011 0.799 4 | 0.030 0.810 0.011 0.150 5 | 0.030 0.940 0.011 0.020 6 | 0.030 0.940 0.011 0.020 7 | 0.939 0.031 0.011 0.020 12 | 0.160 0.550 0.270 0.020 13 | 0.030 0.550 0.011 0.409 14 | 0.160 0.031 0.011 0.799 15 | 0.030 0.940 0.011 0.020 16 | 0.030 0.940 0.011 0.020 17 | 0.030 0.680 0.011 0.279 18 | 0.939 0.031 0.011 0.020 Background probability model 0.229 0.212 0.092 0.176 14 columns Num Motifs: 7 1, 1 39 tcgac ATAGTTAGGCGCTGTTTA actaa 22 1.00 R mgrB genome_pos=1906820-1906867 reference=PMID: 12 2, 1 10 aagtc TGGTTTATCGTTGGTTTA gttgt 27 1.00 F mgtA genome_pos=4465334-4465382 reference=PMID: 12 3, 1 28 cccgc TGGTTTATTTAATGTTTA ccccc 11 1.00 R phoP genome_pos=1189721-1189770 reference=PMID: 12 4, 1 18 aaaac TTGTTTAGAAACGATTGA tagta 35 0.65 F rstA genome_pos=1680092-1680137 reference=PMID: 12 5, 1 14 atgtt TTGTTTATAATTGGTTGA tccta 31 1.00 F slyB genome_pos=1717746-1717796 reference=PMID: 12 6, 1 34 actca TTGTTTAGGGTTTGTTTA atttt 17 1.00 R vboR genome_pos=578153-578200 reference=PMID: 1281 7, 1 17 aggca TTGTTTAGGTTTTGTTTA agtta 34 1.00 F yrbL genome_pos=3346390-3346433 reference=PMID: 12 ******* ******* 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 = -60.44568 Log Fragmentation portion of MAP for motif a = -3.33220 Log Background portion of Map = -328.47960 Log Alignment portion of Map = -31.07708 Log Site/seq portion of Map = 0.00000 Log Null Map = -452.20576 Non Palindromic Map = 17.19261 Log Map = 28.87120 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null Frequency Map = 28.871199 Nearopt Map = 28.049644 Maximal Map = 28.871199 Elapsed time: 0.290000 secs