/local/compbio/programs/bin/Gibbs -PBernoulli purL.fa 16 -n -r -R 1,1,8 -M 1,24 -E 2 -S 40 -p 200 -i 1000 -o purL.16.p200i1000.out -B purL.fa_info-det -P reg.0723.space.pr Gibbs 2.04.016 Dec 23 2003 Data file: purL.fa Output file: purL.16.p200i1000.out Priors file: reg.0723.space.pr Background Composition Model file: purL.fa_info-det 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 site_samp = 0 nMotifLen = 16 nAlphaLen = 4 nNumMotifs = 7 dPseudoCntWt = 0.1 dPseudoSiteWt = 0.8 nMaxIterations = 1000 lSeedVal = 1080254161 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 :purL: Len=395 #2 STYP E_score=0.0 :purL: Len=393 #3 YPES E_score=0.0 :purL: Len=450 #4 VCHO1 E_score=0.0 :purL: Len=444 #5 HINF E_score=0.0 :purL: Len=500 #6 PAER E_score=0.0 :purL: Len=430 #7 SONE E_score=0.0 :purL: Len=385 Processed Sequence Length: 2997 Total sequence length: 2997 ======================== NEAR OPTIMAL RESULTS ======================== ====================================================================== MAP = 5 maybe = 8 discard = 2989 ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 100 . . . 1.3 2 | . 20 80 . 1.0 3 | . . . 100 1.5 4 | . . 100 . 1.5 5 | 100 . . . 1.3 6 | 100 . . . 1.3 7 | 100 . . . 1.3 8 | . . 100 . 1.5 9 | . . . 100 1.5 10 | . 20 . 80 0.9 11 | . 100 . . 1.3 12 | . 100 . . 1.3 13 | . 60 . 40 0.7 14 | . . 100 . 1.5 15 | . 40 . 60 0.7 16 | . 100 . . 1.3 nonsite 27 27 22 23 site 25 27 23 23 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.911 0.033 0.027 0.029 2 | 0.033 0.209 0.729 0.029 3 | 0.033 0.033 0.027 0.906 4 | 0.033 0.033 0.904 0.029 5 | 0.911 0.033 0.027 0.029 6 | 0.911 0.033 0.027 0.029 7 | 0.911 0.033 0.027 0.029 8 | 0.033 0.033 0.904 0.029 9 | 0.033 0.033 0.027 0.906 10 | 0.033 0.209 0.027 0.731 11 | 0.033 0.911 0.027 0.029 12 | 0.033 0.911 0.027 0.029 13 | 0.033 0.560 0.027 0.380 14 | 0.033 0.033 0.904 0.029 15 | 0.033 0.384 0.027 0.555 16 | 0.033 0.911 0.027 0.029 Background probability model 0.272 0.272 0.221 0.235 16 columns Num Motifs: 5 1, 1 304 tttcc ACGCAAACGGTTTCGT cagcg 319 1.00 F ECOL E_score=0.0 :purL: Len=395 2, 1 304 tttct ACGCAAACGGTTTCGT cggcg 319 1.00 F STYP E_score=0.0 :purL: Len=393 3, 1 324 tagat ACGCAAACGGTTTCGT cggcg 339 1.00 F YPES E_score=0.0 :purL: Len=450 4, 1 275 aaatg ACGCAAACGGTTGCTT ttggt 290 1.00 F VCHO1 E_score=0.0 :purL: Len=444 5, 1 426 tttga ATGCAAACGTTTGCTT tgttc 441 1.00 F HINF E_score=0.0 :purL: 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 = -49.22740 Log Fragmentation portion of MAP for motif a = -0.00000 Seed = 1080254161 Difference of Logs of Maps = 30.78391 ============================================================= ====== 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 | 100 . . . 1.4 2 | 16 16 66 . 0.6 3 | 16 . . 83 1.0 4 | . . 100 . 1.6 5 | 100 . . . 1.4 6 | 83 . 16 . 0.9 7 | 83 16 . . 0.9 8 | . . 83 16 1.1 9 | . 16 . 83 1.0 10 | . 33 . 66 0.8 11 | . 100 . . 1.4 12 | . 100 . . 1.4 13 | . 50 . 50 0.7 14 | . . 100 . 1.6 15 | . 33 . 66 0.8 16 | . 100 . . 1.4 nonsite 27 27 22 23 site 25 29 22 22 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.924 0.028 0.023 0.025 2 | 0.178 0.178 0.620 0.025 3 | 0.178 0.028 0.023 0.771 4 | 0.028 0.028 0.919 0.025 5 | 0.924 0.028 0.023 0.025 6 | 0.775 0.028 0.172 0.025 7 | 0.775 0.178 0.023 0.025 8 | 0.028 0.028 0.769 0.174 9 | 0.028 0.178 0.023 0.771 10 | 0.028 0.327 0.023 0.622 11 | 0.028 0.924 0.023 0.025 12 | 0.028 0.924 0.023 0.025 13 | 0.028 0.476 0.023 0.472 14 | 0.028 0.028 0.919 0.025 15 | 0.028 0.327 0.023 0.622 16 | 0.028 0.924 0.023 0.025 Background probability model 0.272 0.272 0.221 0.235 16 columns Num Motifs: 6 1, 1 304 tttcc ACGCAAACGGTTTCGT cagcg 319 1.00 F ECOL E_score=0.0 :purL: Len=395 2, 1 304 tttct ACGCAAACGGTTTCGT cggcg 319 1.00 F STYP E_score=0.0 :purL: Len=393 3, 1 324 tagat ACGCAAACGGTTTCGT cggcg 339 1.00 F YPES E_score=0.0 :purL: Len=450 4, 1 275 aaatg ACGCAAACGGTTGCTT ttggt 290 1.00 F VCHO1 E_score=0.0 :purL: Len=444 5, 1 426 tttga ATGCAAACGTTTGCTT tgttc 441 1.00 F HINF E_score=0.0 :purL: Len=500 7, 1 284 atagg AAACACTGTTTTGCGT aaggt 299 0.52 F SONE E_score=0.0 :purL: Len=385 **************** Difference of Logs of Maps = 30.78391 Log Background portion of Map = -4047.18681 Log Alignment portion of Map = -26.14836 Log Site/seq portion of Map = -8.00973 Log Null Map = -4161.35621 Non Palindromic Map = 29.57085 Max subopt MAP found on seed 35 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 | 100 . . . 1.3 2 | . 20 80 . 1.0 3 | . . . 100 1.5 4 | . . 100 . 1.5 5 | 100 . . . 1.3 6 | 100 . . . 1.3 7 | 100 . . . 1.3 8 | . . 100 . 1.5 9 | . . . 100 1.5 10 | . 20 . 80 0.9 11 | . 100 . . 1.3 12 | . 100 . . 1.3 13 | . 60 . 40 0.7 14 | . . 100 . 1.5 15 | . 40 . 60 0.7 16 | . 100 . . 1.3 nonsite 27 27 22 23 site 25 27 23 23 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.911 0.033 0.027 0.029 2 | 0.033 0.209 0.729 0.029 3 | 0.033 0.033 0.027 0.906 4 | 0.033 0.033 0.904 0.029 5 | 0.911 0.033 0.027 0.029 6 | 0.911 0.033 0.027 0.029 7 | 0.911 0.033 0.027 0.029 8 | 0.033 0.033 0.904 0.029 9 | 0.033 0.033 0.027 0.906 10 | 0.033 0.209 0.027 0.731 11 | 0.033 0.911 0.027 0.029 12 | 0.033 0.911 0.027 0.029 13 | 0.033 0.560 0.027 0.380 14 | 0.033 0.033 0.904 0.029 15 | 0.033 0.384 0.027 0.555 16 | 0.033 0.911 0.027 0.029 Background probability model 0.272 0.272 0.221 0.235 16 columns Num Motifs: 5 1, 1 304 tttcc ACGCAAACGGTTTCGT cagcg 319 1.00 F ECOL E_score=0.0 :purL: Len=395 2, 1 304 tttct ACGCAAACGGTTTCGT cggcg 319 1.00 F STYP E_score=0.0 :purL: Len=393 3, 1 324 tagat ACGCAAACGGTTTCGT cggcg 339 1.00 F YPES E_score=0.0 :purL: Len=450 4, 1 275 aaatg ACGCAAACGGTTGCTT ttggt 290 1.00 F VCHO1 E_score=0.0 :purL: Len=444 5, 1 426 tttga ATGCAAACGTTTGCTT tgttc 441 1.00 F HINF E_score=0.0 :purL: 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 = -49.22740 Log Fragmentation portion of MAP for motif a = -0.00000 Seed = 1080254161 Difference of Logs of Maps = 30.78391 Difference of Logs of Maps = 30.78391 Log Background portion of Map = -4047.18681 Log Alignment portion of Map = -26.14836 Log Site/seq portion of Map = -8.00973 Log Null Map = -4161.35621 Non Palindromic Map = 29.57085 Max subopt MAP found on seed 35 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null Frequency Map = 27.607807 Nearopt Map = 30.783909 Maximal Map = 30.783909 Elapsed time: 85.060000 secs