Gibbs.linux Mtb_7seq.fa 16 -n -r -R 1,1,8 -M 1,24 -E 3 -B Mtb_7seq.fa_info-det -o Mtb_7seq.4.out -S 20 -p 100 -i 1000 -P reg.0805.pr Gibbs 3.01.002 Feb 19 2007 Data file: Mtb_7seq.fa Output file: Mtb_7seq.4.out Priors file: reg.0805.pr Background Composition Model file: Mtb_7seq.fa_info-det 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 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 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 = 0 nMotifLen = 16 nAlphaLen = 4 nNumMotifs = 7 dPseudoCntWt = 0.1 dPseudoSiteWt = 0.8 nMaxIterations = 1000 lSeedVal = 1175886084 nPlateauPeriods = 100 nSeeds = 20 nNumMotifTypes = 1 dCutoff = 0.01 dNearOptDispCutoff = 0.5 RevComplement = 0 glOverlapParam = 0 Max Sites/seq = 3 Min Sites/Seq = 0 Rcutoff factor = 0 Post Plateau Samples = 0 Frag/Shft Per. = 5 Frag width = 24 Sequences to be Searched: _________________________ #1 hspX complement(2278496..2278930) Rv2032 2279127..2280122 5UTR genome coordinates=2278931-2279126 length=196 #2 Rv3130c complement(3494972..3496363) Rv3131 3496548..3497546 5UTR genome coordinates=3496364-3496547 length=184 #3 Rv2005c complement(2250994..2251881) otsB 2252000..2255983 5UTR genome coordinates=2251882-2251999 length=118 #4 Rv2623 2949591..2950484 Rv2622 2948634..2949455 5UTR genome coordinates=2949456-2949590 length=135 #5 narK2 complement(1964181..1965368) Rv1738 1965655..1965939 5UTR genome coordinates=1965369-1965654 length=286 #6 Rv1733c complement(1959853..1960485) Rv1734c complement(1960772..1961014) 5UTR genome coordinates=1960486-1960771 length=286 #7 Rv3127 3492144..3493178 Rv3125c complement(3490473..3491648) 5UTR genome coordinates=3491649-3492143 length=495 Processed Sequence Length: 1700 Total sequence length: 1700 ====================================================================== ======================== NEAR OPTIMAL RESULTS ======================== ====================================================================== MAP = 39 maybe = 45 discard = 1655 ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 15 46 15 23 0.3 2 | 46 . 15 38 0.4 3 | 15 . 15 69 0.5 4 | . . . 100 1.5 5 | . . . 100 1.5 6 | 61 7 30 . 0.7 7 | . . 100 . 1.4 9 | 38 46 . 15 0.7 10 | 46 30 23 . 0.5 12 | . . . 100 1.5 13 | 30 38 15 15 0.3 14 | . . 100 . 1.4 15 | 7 . 92 . 1.1 16 | 7 15 61 15 0.3 17 | . 53 38 7 0.7 18 | 38 15 7 38 0.3 nonsite 21 18 30 29 site 19 15 32 32 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.157 0.447 0.162 0.234 2 | 0.449 0.009 0.162 0.380 3 | 0.157 0.009 0.162 0.672 4 | 0.011 0.009 0.016 0.964 5 | 0.011 0.009 0.016 0.964 6 | 0.595 0.082 0.308 0.015 7 | 0.011 0.009 0.965 0.015 9 | 0.376 0.447 0.016 0.161 10 | 0.449 0.301 0.235 0.015 12 | 0.011 0.009 0.016 0.964 13 | 0.303 0.374 0.162 0.161 14 | 0.011 0.009 0.965 0.015 15 | 0.084 0.009 0.892 0.015 16 | 0.084 0.155 0.600 0.161 17 | 0.011 0.520 0.381 0.088 18 | 0.376 0.155 0.089 0.380 Background probability model 0.213 0.187 0.306 0.294 16 columns Num Motifs: 13 1, 1 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 1, 2 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.92 F hspX complement(2278496..2278930) Rv2032 2279127.. 1, 3 121 ccact TGGGGACCATTGACCCTG ttgtc 138 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 2, 1 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.99 F Rv3130c complement(3494972..3496363) Rv3131 349654 3, 1 75 aatcg GACGGCCAACCGACCATG attgg 92 0.53 F Rv2005c complement(2250994..2251881) otsB 2252000. 4, 1 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.97 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 5, 1 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 5, 2 132 cccct GGCGGACGAATGACCCCA gtggc 149 0.98 F narK2 complement(1964181..1965368) Rv1738 1965655. 5, 3 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 0.99 F narK2 complement(1964181..1965368) Rv1738 1965655. 6, 1 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 0.99 F Rv1733c complement(1959853..1960485) Rv1734c compl 6, 2 46 ggggc TGGGGACGTCGGTCACGA atggc 63 0.97 F Rv1733c complement(1959853..1960485) Rv1734c compl 6, 3 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 7, 1 432 cattg AGAGGACCAATGACCCTA tttga 449 0.99 F Rv3127 3492144..3493178 Rv3125c complement(3490473 ******* ** ******* 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 = -184.70489 Log Fragmentation portion of MAP for motif a = -2.07944 ============================================================= ====== 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 | 16 50 16 16 0.3 2 | 41 . 16 41 0.4 3 | 16 . 8 75 0.7 4 | . . . 100 1.5 5 | . . . 100 1.5 6 | 66 8 25 . 0.8 7 | . . 100 . 1.4 9 | 33 50 . 16 0.7 10 | 50 33 16 . 0.6 12 | . . . 100 1.5 13 | 25 41 16 16 0.2 14 | . . 100 . 1.4 15 | 8 . 91 . 1.1 16 | . 16 66 16 0.5 17 | . 50 41 8 0.6 18 | 41 16 8 33 0.3 nonsite 21 18 30 29 site 18 16 31 32 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.169 0.483 0.174 0.174 2 | 0.405 0.010 0.174 0.410 3 | 0.169 0.010 0.096 0.725 4 | 0.012 0.010 0.017 0.961 5 | 0.012 0.010 0.017 0.961 6 | 0.642 0.089 0.253 0.016 7 | 0.012 0.010 0.962 0.016 9 | 0.327 0.483 0.017 0.174 10 | 0.484 0.325 0.174 0.016 12 | 0.012 0.010 0.017 0.961 13 | 0.248 0.404 0.174 0.174 14 | 0.012 0.010 0.962 0.016 15 | 0.090 0.010 0.883 0.016 16 | 0.012 0.168 0.647 0.174 17 | 0.012 0.483 0.411 0.095 18 | 0.405 0.168 0.096 0.331 Background probability model 0.213 0.187 0.306 0.294 16 columns Num Motifs: 12 1, 1 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 1, 2 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.99 F hspX complement(2278496..2278930) Rv2032 2279127.. 1, 3 121 ccact TGGGGACCATTGACCCTG ttgtc 138 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 2, 1 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.98 F Rv3130c complement(3494972..3496363) Rv3131 349654 4, 1 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.96 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 5, 1 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 5, 2 132 cccct GGCGGACGAATGACCCCA gtggc 149 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 5, 3 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 6, 1 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 6, 2 46 ggggc TGGGGACGTCGGTCACGA atggc 63 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 6, 3 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 7, 1 432 cattg AGAGGACCAATGACCCTA tttga 449 0.97 F Rv3127 3492144..3493178 Rv3125c complement(3490473 ******* ** ******* Log Background portion of Map = -2047.72700 Log Alignment portion of Map = -62.93941 Log Site/seq portion of Map = -7.51929 Log Null Map = -2335.94494 Non Palindromic Map = 6.24257 Log Map = 30.97490 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 | 15 46 15 23 0.3 2 | 46 . 15 38 0.4 3 | 15 . 15 69 0.5 4 | . . . 100 1.5 5 | . . . 100 1.5 6 | 61 7 30 . 0.7 7 | . . 100 . 1.4 9 | 38 46 . 15 0.7 10 | 46 30 23 . 0.5 12 | . . . 100 1.5 13 | 30 38 15 15 0.3 14 | . . 100 . 1.4 15 | 7 . 92 . 1.1 16 | 7 15 61 15 0.3 17 | . 53 38 7 0.7 18 | 38 15 7 38 0.3 nonsite 21 18 30 29 site 19 15 32 32 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.157 0.447 0.162 0.234 2 | 0.449 0.009 0.162 0.380 3 | 0.157 0.009 0.162 0.672 4 | 0.011 0.009 0.016 0.964 5 | 0.011 0.009 0.016 0.964 6 | 0.595 0.082 0.308 0.015 7 | 0.011 0.009 0.965 0.015 9 | 0.376 0.447 0.016 0.161 10 | 0.449 0.301 0.235 0.015 12 | 0.011 0.009 0.016 0.964 13 | 0.303 0.374 0.162 0.161 14 | 0.011 0.009 0.965 0.015 15 | 0.084 0.009 0.892 0.015 16 | 0.084 0.155 0.600 0.161 17 | 0.011 0.520 0.381 0.088 18 | 0.376 0.155 0.089 0.380 Background probability model 0.213 0.187 0.306 0.294 16 columns Num Motifs: 13 1, 1 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 1, 2 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.99 F hspX complement(2278496..2278930) Rv2032 2279127.. 1, 3 121 ccact TGGGGACCATTGACCCTG ttgtc 138 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 2, 1 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.98 F Rv3130c complement(3494972..3496363) Rv3131 349654 3, 1 75 aatcg GACGGCCAACCGACCATG attgg 92 0.37 F Rv2005c complement(2250994..2251881) otsB 2252000. 4, 1 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.96 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 5, 1 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 5, 2 132 cccct GGCGGACGAATGACCCCA gtggc 149 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 5, 3 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 6, 1 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 6, 2 46 ggggc TGGGGACGTCGGTCACGA atggc 63 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 6, 3 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 7, 1 432 cattg AGAGGACCAATGACCCTA tttga 449 0.97 F Rv3127 3492144..3493178 Rv3125c complement(3490473 ******* ** ******* 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 = -184.70489 Log Fragmentation portion of MAP for motif a = -2.07944 Log Background portion of Map = -2047.72700 Log Alignment portion of Map = -62.93941 Log Site/seq portion of Map = -7.51929 Log Null Map = -2335.94494 Non Palindromic Map = 6.24257 Log Map = 30.97490 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null Frequency Map = 27.310450 Nearopt Map = 30.974898 Maximal Map = 30.974898 Elapsed time: 12.110000 secs