/local/compbio/programs/bin/Gibbs glnA.fa 16 -n -r -R 1,1,8 -M 1,24 -E 2 -S 40 -p 200 -i 1000 -o glnA.16.p200i1000.out -B glnA.fa_info-det -P reg.0630.nospace.pr Gibbs 2.06.015 Aug 30 2004 Data file: glnA.fa Output file: glnA.16.p200i1000.out Priors file: reg.0630.nospace.pr Background Composition Model file: glnA.fa_info-det Current directory: /home/mccue/Gibbs_help/cross_species_examples 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 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 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 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. False Calc. def. pseudo wt. False Motif/Recur smpl False Phylogenetic Sampling False site_samp = 0 nMotifLen = 16 nAlphaLen = 4 nNumMotifs = 7 dPseudoCntWt = 0.1 dPseudoSiteWt = 0.8 nMaxIterations = 1000 lSeedVal = 1096309487 nPlateauPeriods = 200 nSeeds = 40 nNumMotifTypes = 1 dCutoff = 0.01 RevComplement = 0 glOverlapParam = 0 Max Sites/seq = 2 Min Sites/Seq = 0 Rcutoff factor = 0.001 Post Plateau Samples = 0 Frag/Shft Per. = 5 Frag width = 24 Sequences to be Searched: _________________________ #1 ECOL E_score=0.0 :glnA: Len=372 #2 STYP E_score=0.0 :glnA: Len=375 #3 YPES E_score=0.0 :glnA: Len=500 #4 VCHO1 E_score=0.0 :glnA: Len=500 #5 HINF E_score=0.0 :glnA: Len=272 #6 PAER E_score=0.0 :glnA: Len=500 #7 SONE E_score=0.0 :glnA: Len=500 Processed Sequence Length: 3019 Total sequence length: 3019 ======================== NEAR OPTIMAL RESULTS ======================== ====================================================================== MAP = 20 maybe = 30 discard = 2989 ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 30 50 10 10 0.2 2 | . . . 100 1.8 3 | . . 100 . 1.8 4 | 100 . . . 1.4 5 | . . 100 . 1.8 6 | . 30 70 . 1.0 7 | 100 . . . 1.4 8 | 60 40 . . 0.7 10 | 70 20 . 10 0.6 11 | . 80 20 . 1.0 12 | 40 . . 60 0.9 13 | . . . 100 1.8 14 | . 90 . 10 1.2 15 | . . . 100 1.8 16 | . . 90 10 1.4 17 | 70 20 10 . 0.6 nonsite 29 26 22 21 site 29 20 25 25 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.300 0.485 0.108 0.107 2 | 0.019 0.018 0.015 0.948 3 | 0.019 0.018 0.949 0.014 4 | 0.954 0.018 0.015 0.014 5 | 0.019 0.018 0.949 0.014 6 | 0.019 0.298 0.669 0.014 7 | 0.954 0.018 0.015 0.014 8 | 0.580 0.391 0.015 0.014 10 | 0.673 0.204 0.015 0.107 11 | 0.019 0.765 0.202 0.014 12 | 0.393 0.018 0.015 0.575 13 | 0.019 0.018 0.015 0.948 14 | 0.019 0.859 0.015 0.107 15 | 0.019 0.018 0.015 0.948 16 | 0.019 0.018 0.856 0.107 17 | 0.673 0.204 0.108 0.014 Background probability model 0.293 0.271 0.225 0.211 16 columns Num Motifs: 10 1, 1 152 gtcat TGCACCAACATGGTGCT taatg 168 1.00 F ECOL E_score=0.0 :glnA: Len=372 1, 2 184 attga AGCACTATATTGGTGCA acatt 200 1.00 F ECOL E_score=0.0 :glnA: Len=372 2, 1 152 tctat TGCACCAATGTGGTGCT taatg 168 1.00 F STYP E_score=0.0 :glnA: Len=375 2, 2 184 attga AGCACTATTTTGGTGCA acata 200 1.00 F STYP E_score=0.0 :glnA: Len=375 3, 1 94 atccc TGCACCAAAATAGTGCC caacg 110 1.00 F YPES E_score=0.0 :glnA: Len=500 3, 2 126 aatga GGCACCAAAATAGTGCA atata 142 1.00 F YPES E_score=0.0 :glnA: Len=500 4, 1 279 gcata CGCACCATGATAGTGCA actga 295 1.00 F VCHO1 E_score=0.0 :glnA: Len=500 6, 1 273 catgg AGCACCATAACGGTGCA cccga 289 1.00 F PAER E_score=0.0 :glnA: Len=500 7, 1 255 gtcac TGCACTAAAATGGGGGA cgaac 271 1.00 F SONE E_score=0.0 :glnA: Len=500 7, 2 322 acaaa TGCACCAACACAGTGCA atcaa 338 1.00 F SONE E_score=0.0 :glnA: Len=500 ******** ******** Column 1 : Sequence Number, Site Number Column 2 : Left End Location Column 4 : Motif Element Column 5 : Right End Location Column 6 : Probability of Element Column 7 : Forward Motif (F) or Reverse Complement (R) Column 8 : Sequence Description from Fast A input Log Motif portion of MAP for motif a = -100.17802 Log Fragmentation portion of MAP for motif a = -0.00000 Seed = 1096309487 Difference of Logs of Maps = 56.74770 ============================================================= ====== 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 1000 iterations Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 33 44 11 11 0.1 2 | . . . 100 1.8 3 | . . 100 . 1.7 4 | 100 . . . 1.4 5 | . . 100 . 1.7 6 | . 22 77 . 1.1 7 | 100 . . . 1.4 8 | 55 44 . . 0.6 10 | 66 22 . 11 0.5 11 | . 77 22 . 0.9 12 | 44 . . 55 0.8 13 | . . . 100 1.8 14 | . 100 . . 1.5 15 | . . . 100 1.8 16 | . . 100 . 1.7 17 | 66 22 11 . 0.5 nonsite 29 26 22 21 site 29 20 26 23 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.330 0.432 0.119 0.118 2 | 0.021 0.019 0.016 0.943 3 | 0.021 0.019 0.944 0.015 4 | 0.949 0.019 0.016 0.015 5 | 0.021 0.019 0.944 0.015 6 | 0.021 0.226 0.738 0.015 7 | 0.949 0.019 0.016 0.015 8 | 0.537 0.432 0.016 0.015 10 | 0.640 0.226 0.016 0.118 11 | 0.021 0.741 0.223 0.015 12 | 0.434 0.019 0.016 0.531 13 | 0.021 0.019 0.016 0.943 14 | 0.021 0.947 0.016 0.015 15 | 0.021 0.019 0.016 0.943 16 | 0.021 0.019 0.944 0.015 17 | 0.640 0.226 0.119 0.015 Background probability model 0.293 0.271 0.225 0.211 16 columns Num Motifs: 9 1, 1 152 gtcat TGCACCAACATGGTGCT taatg 168 0.99 F ECOL E_score=0.0 :glnA: Len=372 1, 2 184 attga AGCACTATATTGGTGCA acatt 200 0.99 F ECOL E_score=0.0 :glnA: Len=372 2, 1 152 tctat TGCACCAATGTGGTGCT taatg 168 0.85 F STYP E_score=0.0 :glnA: Len=375 2, 2 184 attga AGCACTATTTTGGTGCA acata 200 0.99 F STYP E_score=0.0 :glnA: Len=375 3, 1 94 atccc TGCACCAAAATAGTGCC caacg 110 0.84 F YPES E_score=0.0 :glnA: Len=500 3, 2 126 aatga GGCACCAAAATAGTGCA atata 142 0.82 F YPES E_score=0.0 :glnA: Len=500 4, 1 279 gcata CGCACCATGATAGTGCA actga 295 1.00 F VCHO1 E_score=0.0 :glnA: Len=500 6, 1 273 catgg AGCACCATAACGGTGCA cccga 289 1.00 F PAER E_score=0.0 :glnA: Len=500 7, 1 322 acaaa TGCACCAACACAGTGCA atcaa 338 0.99 F SONE E_score=0.0 :glnA: Len=500 ******** ******** Difference of Logs of Maps = 56.74770 Log Background portion of Map = -3954.16774 Log Alignment portion of Map = -57.50866 Log Site/seq portion of Map = -10.35628 Log Null Map = -4178.95840 Non Palindromic Map = 42.51077 Max subopt MAP found on seed 5 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 | 33 50 8 8 0.2 2 | . . . 100 1.9 3 | . . 91 8 1.5 4 | 100 . . . 1.5 5 | . 8 91 . 1.5 6 | . 25 75 . 1.1 7 | 91 8 . . 1.2 8 | 58 41 . . 0.7 10 | 66 25 . 8 0.6 11 | . 83 16 . 1.1 12 | 33 . . 66 1.0 13 | . . . 100 1.9 14 | 8 83 . 8 1.0 15 | 8 . . 91 1.5 16 | . 8 83 8 1.1 17 | 66 16 8 8 0.4 nonsite 29 26 22 21 site 29 21 23 25 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.331 0.487 0.091 0.090 2 | 0.016 0.015 0.012 0.957 3 | 0.016 0.015 0.879 0.090 4 | 0.961 0.015 0.012 0.012 5 | 0.016 0.094 0.879 0.012 6 | 0.016 0.251 0.721 0.012 7 | 0.882 0.094 0.012 0.012 8 | 0.567 0.408 0.012 0.012 10 | 0.646 0.251 0.012 0.090 11 | 0.016 0.802 0.170 0.012 12 | 0.331 0.015 0.012 0.642 13 | 0.016 0.015 0.012 0.957 14 | 0.095 0.802 0.012 0.090 15 | 0.095 0.015 0.012 0.878 16 | 0.016 0.094 0.800 0.090 17 | 0.646 0.172 0.091 0.090 Background probability model 0.293 0.271 0.226 0.210 16 columns Num Motifs: 12 1, 1 152 gtcat TGCACCAACATGGTGCT taatg 168 1.00 F ECOL E_score=0.0 :glnA: Len=372 1, 2 184 attga AGCACTATATTGGTGCA acatt 200 1.00 F ECOL E_score=0.0 :glnA: Len=372 2, 1 152 tctat TGCACCAATGTGGTGCT taatg 168 1.00 F STYP E_score=0.0 :glnA: Len=375 2, 2 184 attga AGCACTATTTTGGTGCA acata 200 1.00 F STYP E_score=0.0 :glnA: Len=375 3, 1 94 atccc TGCACCAAAATAGTGCC caacg 110 1.00 F YPES E_score=0.0 :glnA: Len=500 3, 2 126 aatga GGCACCAAAATAGTGCA atata 142 1.00 F YPES E_score=0.0 :glnA: Len=500 4, 1 279 gcata CGCACCATGATAGTGCA actga 295 1.00 F VCHO1 E_score=0.0 :glnA: Len=500 4, 2 300 aactg AGGATCTTTTTGGTGCA caagc 316 0.93 F VCHO1 E_score=0.0 :glnA: Len=500 6, 1 242 tttgc TGCACCAAAATGGAATG atgca 258 0.71 F PAER E_score=0.0 :glnA: Len=500 6, 2 273 catgg AGCACCATAACGGTGCA cccga 289 1.00 F PAER E_score=0.0 :glnA: Len=500 7, 1 255 gtcac TGCACTAAAATGGGGGA cgaac 271 1.00 F SONE E_score=0.0 :glnA: Len=500 7, 2 322 acaaa TGCACCAACACAGTGCA atcaa 338 1.00 F SONE E_score=0.0 :glnA: Len=500 ******** ******** Column 1 : Sequence Number, Site Number Column 2 : Left End Location Column 4 : Motif Element Column 5 : Right End Location Column 6 : Probability of Element Column 7 : Forward Motif (F) or Reverse Complement (R) Column 8 : Sequence Description from Fast A input Log Motif portion of MAP for motif a = -136.82919 Log Fragmentation portion of MAP for motif a = -0.00000 Seed = 1096309487 Difference of Logs of Maps = 57.30925 Difference of Logs of Maps = 57.30925 Log Background portion of Map = -3910.08955 Log Alignment portion of Map = -68.34779 Log Site/seq portion of Map = -6.38261 Log Null Map = -4178.95840 Non Palindromic Map = 41.32408 Max subopt MAP found on seed 5 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null Frequency Map = 53.510790 Nearopt Map = 56.747696 Maximal Map = 57.309250 Elapsed time: 79.590000 secs