Gibbs.linux hypoxia.fa 16,16 -n -r -R 1,1,8,2,1,8 -M 1,24,2,24 -E 3 -S 20 -p 100 -i 1000 -B hypoxia.fa_info-det -o hypoxia.1.out Gibbs 3.01.002 Feb 19 2007 Data file: hypoxia.fa Output file: hypoxia.1.out Background Composition Model file: hypoxia.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 False 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, 16 nAlphaLen = 4 nNumMotifs = 16 ,16 dPseudoCntWt = 0.1 dPseudoSiteWt = 0.8 nMaxIterations = 1000 lSeedVal = 1176146459 nPlateauPeriods = 100 nSeeds = 20 nNumMotifTypes = 2 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 = 24,24 Sequences to be Searched: _________________________ #1 Rv0079 88202..89023 Rv0078 86526..87131 5UTR genome coordinates=87132-88201 length=1070 #2 Rv0081 89573..89917 Rv0080 89020..89478 5UTR genome coordinates=89479-89572 length=94 #3 Rv0569 661001..661267 Rv0568 659448..660866 5UTR genome coordinates=660867-661000 length=134 #4 Rv0572c complement(665040..665381) Rv0573c complement(665849..667240) 5UTR genome coordinates=665382-665848 length=467 #5 Rv0574c complement(667250..668392) Rv0575c complement(668577..669743) 5UTR genome coordinates=668393-668576 length=184 #6 Rv1264 1411892..1413085 amiB2 1410429..1411817 5UTR genome coordinates=1411818-1411891 length=74 #7 Rv1592c complement(1792398..1793738) Rv1593c complement(1793995..1794705) 5UTR genome coordinates=1793739-1793994 length=256 #8 Rv1733c complement(1959853..1960485) Rv1734c complement(1960772..1961014) 5UTR genome coordinates=1960486-1960771 length=286 #9 Rv1734c complement(1960772..1961014) Rv1735c complement(1961289..1961786) 5UTR genome coordinates=1961015-1961288 length=274 #10 narK2 complement(1964181..1965368) Rv1738 1965655..1965939 5UTR genome coordinates=1965369-1965654 length=286 #11 Rv1739c complement(1965953..1967635) Rv1740 1967703..1967915 5UTR genome coordinates=1967636-1967702 length=67 #12 Rv1813c complement(2055679..2056110) Rv1814 2056519..2057421 5UTR genome coordinates=2056111-2056518 length=408 #13 ctpF 2240157..2242874 Rv1996 2239002..2239955 5UTR genome coordinates=2239956-2240156 length=201 #14 Rv1998c complement(2242943..2243719) Rv1999c complement(2243814..2245136) 5UTR genome coordinates=2243720-2243813 length=94 #15 Rv2003c complement(2248561..2249418) Rv2004c complement(2249476..2250972) 5UTR genome coordinates=2249419-2249475 length=57 #16 Rv2005c complement(2250994..2251881) otsB 2252000..2255983 5UTR genome coordinates=2251882-2251999 length=118 #17 fdxA complement(2256082..2256426) Rv2008c complement(2256615..2257940) 5UTR genome coordinates=2256427-2256614 length=188 #18 hspX complement(2278496..2278930) Rv2032 2279127..2280122 5UTR genome coordinates=2278931-2279126 length=196 #19 proA complement(2724228..2725475) ahpC 2726191..2726778 5UTR genome coordinates=2725476-2726190 length=715 #20 Rv2623 2949591..2950484 Rv2622 2948634..2949455 5UTR genome coordinates=2949456-2949590 length=135 #21 Rv2625c complement(2951320..2952501) Rv2626c complement(2952560..2952991) 5UTR genome coordinates=2952502-2952559 length=58 #22 Rv2626c complement(2952560..2952991) Rv2627c complement(2953505..2954746) 5UTR genome coordinates=2952992-2953504 length=513 #23 Rv2627c complement(2953505..2954746) Rv2628 2955056..2955418 5UTR genome coordinates=2954747-2955055 length=309 #24 Rv2629 2955765..2956889 Rv2628 2955056..2955418 5UTR genome coordinates=2955419-2955764 length=346 #25 Rv2659c complement(2979688..2980815) Rv2660c complement(2980960..2981187) 5UTR genome coordinates=2980816-2980959 length=144 #26 Rv3127 3492144..3493178 Rv3125c complement(3490473..3491648) 5UTR genome coordinates=3491649-3492143 length=495 #27 Rv3128c complement(3493165..3494178) Rv3129 3494657..3494989 5UTR genome coordinates=3494179-3494656 length=478 #28 Rv3130c complement(3494972..3496363) Rv3131 3496548..3497546 5UTR genome coordinates=3496364-3496547 length=184 #29 Rv3133c complement(3499259..3499912) Rv3134c complement(3499940..3500746) 5UTR genome coordinates=3499913-3499939 length=27 #30 Rv3134c complement(3499940..3500746) PPE__e290950 3501331..3501729 5UTR genome coordinates=3500747-3501330 length=584 #31 bfrB 4314175..4314720 Rv3840 4313564..4313977 5UTR genome coordinates=4313978-4314174 length=197 #32 pcnA complement(4391628..4393070) Rv3908 4393446..4394192 5UTR genome coordinates=4393071-4393445 length=375 Processed Sequence Length: 9014 Total sequence length: 9014 ====================================================================== ======================== NEAR OPTIMAL RESULTS ======================== ====================================================================== MAP = 153 maybe = 297 discard = 17731 ============================================================= ====== Results by Sequence ===== ============================================================= 1, 1, 0 983 ttggc ATGGGACTTTCGGCCCTG tccgc 1000 0.98 F Rv0079 88202..89023 Rv0078 86526..87131 5UTR ge 3, 1, 1 17 atccg CATGGGGTCGCCCAGCGG gtccc 34 0.47 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 3, 2, 0 41 tcccg AGGGGACTTTTGGCCACC ggcgc 58 0.92 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 3, 3, 0 65 gcgct GGTGGCCTACTGCCCTCC cgccg 82 0.02 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 5, 1, 1 64 cacgt CATACGATCGGCCGGCGG cggcc 81 0.92 F Rv0574c complement(667250..668392) Rv0575c complem 5, 2, 0 94 gtggg TGGGGCCGAAGGTCCTCA agacc 111 1.00 F Rv0574c complement(667250..668392) Rv0575c complem 8, 1, 0 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 0.96 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 2, 0 46 ggggc TGGGGACGTCGGTCACGA atggc 63 0.93 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 3, 0 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 0.99 F Rv1733c complement(1959853..1960485) Rv1734c compl 9, 1, 0 31 gagcc CGGGGACTTCGGTCCCCA gagcc 48 0.99 F Rv1734c complement(1960772..1961014) Rv1735c compl 10, 1, 0 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 0.99 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 2, 0 132 cccct GGCGGACGAATGACCCCA gtggc 149 0.90 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 3, 0 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 0.92 F narK2 complement(1964181..1965368) Rv1738 1965655. 12, 1, 1 63 acgcg CAGTGGATGCGTCGAAGG gtcaa 80 0.63 F Rv1813c complement(2055679..2056110) Rv1814 205651 12, 2, 0 254 ccggg TAGGGCATAAAGTCTCTA acagc 271 0.95 F Rv1813c complement(2055679..2056110) Rv1814 205651 12, 3, 0 287 ccgga TAGGGAACAACGGCCTTC gggca 304 0.96 F Rv1813c complement(2055679..2056110) Rv1814 205651 13, 1, 0 91 cagcg CTGGACCGTAGGTCCCTG cagtg 108 0.64 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 2, 0 113 gcagt GGATGACTTACGGCCCTG atcca 130 0.93 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 3, 1 167 gccaa CCGTCGGTTGAGCGTCTG gctgc 184 0.93 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 16, 1, 0 53 cggtc ATGAGGCTTTAGTCCCCA atcgg 70 0.70 F Rv2005c complement(2250994..2251881) otsB 2252000. 16, 2, 1 73 ccaat CGGACGGCCAACCGACCA tgatt 90 0.52 F Rv2005c complement(2250994..2251881) otsB 2252000. 16, 3, 1 92 accat GATTGGATTCGACGCCCG aatcc 109 0.20 F Rv2005c complement(2250994..2251881) otsB 2252000. 17, 1, 1 25 cgatg CCGAGGATCGCGCCTATC caaag 42 0.29 F fdxA complement(2256082..2256426) Rv2008c compleme 17, 2, 0 59 accgg AAAGGACCAAAGGCCTTA ttcgt 76 0.99 F fdxA complement(2256082..2256426) Rv2008c compleme 17, 3, 1 124 aaacc GGGGCGGTTCACCCGACC gccag 141 0.56 F fdxA complement(2256082..2256426) Rv2008c compleme 18, 1, 0 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 2, 0 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.63 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 3, 0 121 ccact TGGGGACCATTGACCCTG ttgtc 138 0.99 F hspX complement(2278496..2278930) Rv2032 2279127.. 20, 1, 0 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.91 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 20, 2, 0 28 tgggc TAGTGACAAACGCCTCCT gagca 45 0.66 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 20, 3, 1 105 ccgag CGGGCGATCAGCCAACGA cagga 122 0.21 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 21, 1, 1 38 tcgtg CCGGCGGATGATCCGAGG tcg 55 0.73 F Rv2625c complement(2951320..2952501) Rv2626c compl 22, 1, 0 72 aacac TAGGGTCGTTTGACCCGT gggcc 89 0.95 F Rv2626c complement(2952560..2952991) Rv2627c compl 22, 2, 1 93 gtggg CCGCGGGTCGATGGACCC gtact 110 0.75 F Rv2626c complement(2952560..2952991) Rv2627c compl 22, 3, 0 238 gatag TGATGCCGATCGGCCCCG atcgg 255 0.86 F Rv2626c complement(2952560..2952991) Rv2627c compl 23, 1, 0 35 cgcgt TAGGGACTTACGTCCCGC cggaa 52 1.00 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 2, 0 104 gttgt GGTGGCCCAAGTGCCCTA aggtg 121 0.66 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 3, 0 274 cagtg AAGTGACGAAAGACCCCA gtgga 291 0.99 F Rv2627c complement(2953505..2954746) Rv2628 295505 24, 1, 0 47 ccggt GGATGACTTTGGTCCCTA tgcct 64 0.99 F Rv2629 2955765..2956889 Rv2628 2955056..2955418 26, 1, 1 331 gcgct CAGCTCATCGACCGCAGC atcga 348 0.69 F Rv3127 3492144..3493178 Rv3125c complement(3490473 26, 2, 1 352 gcatc GAGCCGGTCCAGCGCCGC gacca 369 0.90 F Rv3127 3492144..3493178 Rv3125c complement(3490473 26, 3, 0 432 cattg AGAGGACCAATGACCCTA tttga 449 0.97 F Rv3127 3492144..3493178 Rv3125c complement(3490473 28, 1, 0 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.98 F Rv3130c complement(3494972..3496363) Rv3131 349654 30, 1, 0 74 tctcc CAGGGGCGTTGGTCCCCA cctga 91 0.99 F Rv3134c complement(3499940..3500746) PPE__e290950 30, 2, 0 95 cacct GAGGGCCGTTAGTCCTTA tcgac 112 1.00 F Rv3134c complement(3499940..3500746) PPE__e290950 30, 3, 1 257 aacca GCGGCCGTCCATCGGCTG catat 274 0.83 F Rv3134c complement(3499940..3500746) PPE__e290950 46 motifs Column 1 : Sequence Number, Site Number Column 2 : Motif type Column 3 : 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 ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 21 40 15 21 0.2 2 | 43 9 6 40 0.4 3 | 18 6 3 71 0.6 4 | 3 15 . 81 0.9 5 | 3 . . 96 1.3 6 | 56 6 31 6 0.6 7 | 6 . 93 . 1.2 9 | 40 53 . 6 0.9 10 | 50 37 12 . 0.8 12 | . 3 . 96 1.3 13 | 15 43 12 28 0.2 14 | . . 100 . 1.4 15 | 3 6 90 . 1.1 16 | 3 21 68 6 0.5 17 | . 46 43 9 0.6 18 | 46 12 15 25 0.3 nonsite 19 19 31 30 site 19 18 30 30 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.217 0.396 0.164 0.223 2 | 0.426 0.098 0.074 0.401 3 | 0.188 0.069 0.045 0.699 4 | 0.039 0.158 0.015 0.788 5 | 0.039 0.009 0.015 0.937 6 | 0.545 0.069 0.313 0.074 7 | 0.069 0.009 0.908 0.014 9 | 0.396 0.515 0.015 0.074 10 | 0.485 0.366 0.134 0.014 12 | 0.009 0.039 0.015 0.937 13 | 0.158 0.426 0.134 0.282 14 | 0.009 0.009 0.967 0.014 15 | 0.039 0.069 0.878 0.014 16 | 0.039 0.218 0.670 0.074 17 | 0.009 0.456 0.432 0.104 18 | 0.455 0.128 0.164 0.253 Background probability model 0.191 0.195 0.312 0.302 16 columns Num Motifs: 32 1, 1 983 ttggc ATGGGACTTTCGGCCCTG tccgc 1000 0.98 F Rv0079 88202..89023 Rv0078 86526..87131 5UTR ge 3, 1 41 tcccg AGGGGACTTTTGGCCACC ggcgc 58 0.92 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 3, 2 65 gcgct GGTGGCCTACTGCCCTCC cgccg 82 0.02 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 5, 1 94 gtggg TGGGGCCGAAGGTCCTCA agacc 111 1.00 F Rv0574c complement(667250..668392) Rv0575c complem 8, 1 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 0.96 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 2 46 ggggc TGGGGACGTCGGTCACGA atggc 63 0.93 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 3 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 0.99 F Rv1733c complement(1959853..1960485) Rv1734c compl 9, 1 31 gagcc CGGGGACTTCGGTCCCCA gagcc 48 0.99 F Rv1734c complement(1960772..1961014) Rv1735c compl 10, 1 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 0.99 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 2 132 cccct GGCGGACGAATGACCCCA gtggc 149 0.90 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 3 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 0.92 F narK2 complement(1964181..1965368) Rv1738 1965655. 12, 1 254 ccggg TAGGGCATAAAGTCTCTA acagc 271 0.95 F Rv1813c complement(2055679..2056110) Rv1814 205651 12, 2 287 ccgga TAGGGAACAACGGCCTTC gggca 304 0.96 F Rv1813c complement(2055679..2056110) Rv1814 205651 13, 1 91 cagcg CTGGACCGTAGGTCCCTG cagtg 108 0.64 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 2 113 gcagt GGATGACTTACGGCCCTG atcca 130 0.93 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 16, 1 53 cggtc ATGAGGCTTTAGTCCCCA atcgg 70 0.70 F Rv2005c complement(2250994..2251881) otsB 2252000. 17, 1 59 accgg AAAGGACCAAAGGCCTTA ttcgt 76 0.99 F fdxA complement(2256082..2256426) Rv2008c compleme 18, 1 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 2 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.63 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 3 121 ccact TGGGGACCATTGACCCTG ttgtc 138 0.99 F hspX complement(2278496..2278930) Rv2032 2279127.. 20, 1 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.91 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 20, 2 28 tgggc TAGTGACAAACGCCTCCT gagca 45 0.66 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 22, 1 72 aacac TAGGGTCGTTTGACCCGT gggcc 89 0.95 F Rv2626c complement(2952560..2952991) Rv2627c compl 22, 2 238 gatag TGATGCCGATCGGCCCCG atcgg 255 0.86 F Rv2626c complement(2952560..2952991) Rv2627c compl 23, 1 35 cgcgt TAGGGACTTACGTCCCGC cggaa 52 1.00 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 2 104 gttgt GGTGGCCCAAGTGCCCTA aggtg 121 0.66 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 3 274 cagtg AAGTGACGAAAGACCCCA gtgga 291 0.99 F Rv2627c complement(2953505..2954746) Rv2628 295505 24, 1 47 ccggt GGATGACTTTGGTCCCTA tgcct 64 0.99 F Rv2629 2955765..2956889 Rv2628 2955056..2955418 26, 1 432 cattg AGAGGACCAATGACCCTA tttga 449 0.97 F Rv3127 3492144..3493178 Rv3125c complement(3490473 28, 1 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.98 F Rv3130c complement(3494972..3496363) Rv3131 349654 30, 1 74 tctcc CAGGGGCGTTGGTCCCCA cctga 91 0.99 F Rv3134c complement(3499940..3500746) PPE__e290950 30, 2 95 cacct GAGGGCCGTTAGTCCTTA tcgac 112 1.00 F Rv3134c complement(3499940..3500746) PPE__e290950 ******* ** ******* 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 = -442.20977 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 | 22 41 16 19 0.2 2 | 45 9 6 38 0.4 3 | 19 3 3 74 0.7 4 | 3 16 . 80 0.9 5 | 3 . . 96 1.3 6 | 58 6 29 6 0.6 7 | 6 . 93 . 1.2 9 | 38 54 . 6 0.9 10 | 51 38 9 . 0.8 12 | . 3 . 96 1.3 13 | 16 45 9 29 0.3 14 | . . 100 . 1.4 15 | 3 6 90 . 1.0 16 | 3 19 70 6 0.5 17 | . 48 41 9 0.6 18 | 48 12 12 25 0.3 nonsite 19 19 31 30 site 19 19 30 30 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.224 0.408 0.169 0.199 2 | 0.439 0.101 0.077 0.383 3 | 0.193 0.040 0.046 0.720 4 | 0.040 0.163 0.015 0.782 5 | 0.040 0.009 0.015 0.935 6 | 0.561 0.071 0.291 0.076 7 | 0.071 0.009 0.905 0.015 9 | 0.377 0.531 0.015 0.076 10 | 0.500 0.378 0.107 0.015 12 | 0.009 0.040 0.015 0.935 13 | 0.163 0.439 0.107 0.291 14 | 0.009 0.009 0.966 0.015 15 | 0.040 0.071 0.874 0.015 16 | 0.040 0.194 0.690 0.076 17 | 0.009 0.470 0.414 0.107 18 | 0.469 0.132 0.138 0.260 Background probability model 0.191 0.195 0.312 0.302 16 columns Num Motifs: 31 1, 1 983 ttggc ATGGGACTTTCGGCCCTG tccgc 1000 0.59 F Rv0079 88202..89023 Rv0078 86526..87131 5UTR ge 3, 1 41 tcccg AGGGGACTTTTGGCCACC ggcgc 58 0.71 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 5, 1 94 gtggg TGGGGCCGAAGGTCCTCA agacc 111 0.99 F Rv0574c complement(667250..668392) Rv0575c complem 8, 1 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 0.98 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 2 46 ggggc TGGGGACGTCGGTCACGA atggc 63 0.97 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 3 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 9, 1 31 gagcc CGGGGACTTCGGTCCCCA gagcc 48 0.97 F Rv1734c complement(1960772..1961014) Rv1735c compl 10, 1 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 2 132 cccct GGCGGACGAATGACCCCA gtggc 149 0.94 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 3 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 0.94 F narK2 complement(1964181..1965368) Rv1738 1965655. 12, 1 254 ccggg TAGGGCATAAAGTCTCTA acagc 271 0.70 F Rv1813c complement(2055679..2056110) Rv1814 205651 12, 2 287 ccgga TAGGGAACAACGGCCTTC gggca 304 0.80 F Rv1813c complement(2055679..2056110) Rv1814 205651 13, 1 91 cagcg CTGGACCGTAGGTCCCTG cagtg 108 0.58 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 2 113 gcagt GGATGACTTACGGCCCTG atcca 130 0.93 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 16, 1 53 cggtc ATGAGGCTTTAGTCCCCA atcgg 70 0.54 F Rv2005c complement(2250994..2251881) otsB 2252000. 17, 1 59 accgg AAAGGACCAAAGGCCTTA ttcgt 76 0.98 F fdxA complement(2256082..2256426) Rv2008c compleme 18, 1 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 2 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.81 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 3 121 ccact TGGGGACCATTGACCCTG ttgtc 138 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 20, 1 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.91 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 20, 2 28 tgggc TAGTGACAAACGCCTCCT gagca 45 0.69 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 22, 1 72 aacac TAGGGTCGTTTGACCCGT gggcc 89 0.89 F Rv2626c complement(2952560..2952991) Rv2627c compl 22, 2 238 gatag TGATGCCGATCGGCCCCG atcgg 255 0.73 F Rv2626c complement(2952560..2952991) Rv2627c compl 23, 1 35 cgcgt TAGGGACTTACGTCCCGC cggaa 52 1.00 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 2 104 gttgt GGTGGCCCAAGTGCCCTA aggtg 121 0.62 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 3 274 cagtg AAGTGACGAAAGACCCCA gtgga 291 0.99 F Rv2627c complement(2953505..2954746) Rv2628 295505 24, 1 47 ccggt GGATGACTTTGGTCCCTA tgcct 64 0.95 F Rv2629 2955765..2956889 Rv2628 2955056..2955418 26, 1 432 cattg AGAGGACCAATGACCCTA tttga 449 0.92 F Rv3127 3492144..3493178 Rv3125c complement(3490473 28, 1 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.92 F Rv3130c complement(3494972..3496363) Rv3131 349654 30, 1 74 tctcc CAGGGGCGTTGGTCCCCA cctga 91 0.98 F Rv3134c complement(3499940..3500746) PPE__e290950 30, 2 95 cacct GAGGGCCGTTAGTCCTTA tcgac 112 0.99 F Rv3134c complement(3499940..3500746) PPE__e290950 ******* ** ******* ------------------------------------------------------------------------- MOTIF b Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | . . 71 28 0.6 2 | 42 . 35 21 0.3 3 | . 21 . 78 0.8 5 | . 7 57 35 0.3 6 | . . 14 85 0.8 7 | 42 . . 57 0.7 8 | 7 85 7 . 1.2 9 | . 28 64 7 0.5 10 | 14 . 35 50 0.3 11 | 57 . 14 28 0.5 12 | 7 28 42 21 0.1 13 | . . 92 7 1.0 14 | 14 . 21 64 0.4 16 | 35 . 64 . 0.7 17 | . 21 28 50 0.2 18 | 14 . 35 50 0.3 nonsite 19 19 31 30 site 14 12 36 36 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.020 0.020 0.673 0.288 2 | 0.404 0.020 0.353 0.224 3 | 0.020 0.212 0.032 0.736 5 | 0.020 0.084 0.545 0.352 6 | 0.020 0.020 0.160 0.800 7 | 0.404 0.020 0.032 0.544 8 | 0.084 0.789 0.096 0.031 9 | 0.020 0.276 0.609 0.095 10 | 0.148 0.020 0.353 0.480 11 | 0.532 0.020 0.160 0.288 12 | 0.084 0.276 0.417 0.224 13 | 0.020 0.020 0.865 0.095 14 | 0.148 0.020 0.224 0.608 16 | 0.340 0.020 0.609 0.031 17 | 0.020 0.212 0.288 0.480 18 | 0.148 0.020 0.353 0.480 Background probability model 0.191 0.195 0.312 0.302 16 columns Num Motifs: 14 3, 1 17 atccg CATGGGGTCGCCCAGCGG gtccc 34 0.47 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 5, 1 64 cacgt CATACGATCGGCCGGCGG cggcc 81 0.92 F Rv0574c complement(667250..668392) Rv0575c complem 12, 1 63 acgcg CAGTGGATGCGTCGAAGG gtcaa 80 0.63 F Rv1813c complement(2055679..2056110) Rv1814 205651 13, 1 167 gccaa CCGTCGGTTGAGCGTCTG gctgc 184 0.93 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 16, 1 73 ccaat CGGACGGCCAACCGACCA tgatt 90 0.52 F Rv2005c complement(2250994..2251881) otsB 2252000. 16, 2 92 accat GATTGGATTCGACGCCCG aatcc 109 0.20 F Rv2005c complement(2250994..2251881) otsB 2252000. 17, 1 25 cgatg CCGAGGATCGCGCCTATC caaag 42 0.29 F fdxA complement(2256082..2256426) Rv2008c compleme 17, 2 124 aaacc GGGGCGGTTCACCCGACC gccag 141 0.56 F fdxA complement(2256082..2256426) Rv2008c compleme 20, 1 105 ccgag CGGGCGATCAGCCAACGA cagga 122 0.21 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 21, 1 38 tcgtg CCGGCGGATGATCCGAGG tcg 55 0.73 F Rv2625c complement(2951320..2952501) Rv2626c compl 22, 1 93 gtggg CCGCGGGTCGATGGACCC gtact 110 0.75 F Rv2626c complement(2952560..2952991) Rv2627c compl 26, 1 331 gcgct CAGCTCATCGACCGCAGC atcga 348 0.69 F Rv3127 3492144..3493178 Rv3125c complement(3490473 26, 2 352 gcatc GAGCCGGTCCAGCGCCGC gacca 369 0.90 F Rv3127 3492144..3493178 Rv3125c complement(3490473 30, 1 257 aacca GCGGCCGTCCATCGGCTG catat 274 0.83 F Rv3134c complement(3499940..3500746) PPE__e290950 *** ********** *** 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 b = -224.40099 Log Fragmentation portion of MAP for motif b = -2.07944 ============================================================= ====== ELEMENTS OCCURRING GREATER THAN 50% OF THE TIME ===== ====== Motif b ===== ============================================================= 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 . 0.4 2 | 50 . 50 . 0.3 3 | . 50 . 50 0.3 5 | . . 100 . 0.4 6 | . . . 100 0.5 7 | 50 . . 50 0.3 8 | . 100 . . 0.7 9 | . 50 50 . 0.2 10 | . . . 100 0.5 11 | 50 . . 50 0.3 12 | . . 50 50 0.2 13 | . . 100 . 0.4 14 | . . . 100 0.5 16 | . . 100 . 0.4 17 | . 50 . 50 0.3 18 | . . . 100 0.5 nonsite 19 19 31 30 site 9 15 34 40 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.085 0.086 0.695 0.135 2 | 0.362 0.086 0.417 0.135 3 | 0.085 0.363 0.139 0.413 5 | 0.085 0.086 0.695 0.135 6 | 0.085 0.086 0.139 0.691 7 | 0.362 0.086 0.139 0.413 8 | 0.085 0.641 0.139 0.135 9 | 0.085 0.363 0.417 0.135 10 | 0.085 0.086 0.139 0.691 11 | 0.362 0.086 0.139 0.413 12 | 0.085 0.086 0.417 0.413 13 | 0.085 0.086 0.695 0.135 14 | 0.085 0.086 0.139 0.691 16 | 0.085 0.086 0.695 0.135 17 | 0.085 0.363 0.139 0.413 18 | 0.085 0.086 0.139 0.691 Background probability model 0.191 0.195 0.312 0.302 16 columns Num Motifs: 2 5, 1 64 cacgt CATACGATCGGCCGGCGG cggcc 81 0.55 F Rv0574c complement(667250..668392) Rv0575c complem 13, 1 167 gccaa CCGTCGGTTGAGCGTCTG gctgc 184 0.61 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 *** ********** *** Log Background portion of Map = -11271.37876 Log Alignment portion of Map = -251.26835 Log Site/seq portion of Map = -40.56745 Log Null Map = -12276.71642 Non Palindromic Map = 3.69280 Log Map = 42.73221 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null ============================================================= ====== Results by Sequence ===== ====== ELEMENTS OCCURRING GREATER THAN 50% OF THE TIME ===== ============================================================= 1, 1, 0 983 ttggc ATGGGACTTTCGGCCCTG tccgc 1000 0.59 F Rv0079 88202..89023 Rv0078 86526..87131 5UTR ge 3, 1, 0 41 tcccg AGGGGACTTTTGGCCACC ggcgc 58 0.71 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 5, 1, 1 64 cacgt CATACGATCGGCCGGCGG cggcc 81 0.55 F Rv0574c complement(667250..668392) Rv0575c complem 5, 2, 0 94 gtggg TGGGGCCGAAGGTCCTCA agacc 111 0.99 F Rv0574c complement(667250..668392) Rv0575c complem 8, 1, 0 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 0.98 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 2, 0 46 ggggc TGGGGACGTCGGTCACGA atggc 63 0.97 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 3, 0 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 9, 1, 0 31 gagcc CGGGGACTTCGGTCCCCA gagcc 48 0.97 F Rv1734c complement(1960772..1961014) Rv1735c compl 10, 1, 0 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 2, 0 132 cccct GGCGGACGAATGACCCCA gtggc 149 0.94 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 3, 0 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 0.94 F narK2 complement(1964181..1965368) Rv1738 1965655. 12, 1, 0 254 ccggg TAGGGCATAAAGTCTCTA acagc 271 0.70 F Rv1813c complement(2055679..2056110) Rv1814 205651 12, 2, 0 287 ccgga TAGGGAACAACGGCCTTC gggca 304 0.80 F Rv1813c complement(2055679..2056110) Rv1814 205651 13, 1, 0 91 cagcg CTGGACCGTAGGTCCCTG cagtg 108 0.58 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 2, 0 113 gcagt GGATGACTTACGGCCCTG atcca 130 0.93 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 3, 1 167 gccaa CCGTCGGTTGAGCGTCTG gctgc 184 0.61 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 16, 1, 0 53 cggtc ATGAGGCTTTAGTCCCCA atcgg 70 0.54 F Rv2005c complement(2250994..2251881) otsB 2252000. 17, 1, 0 59 accgg AAAGGACCAAAGGCCTTA ttcgt 76 0.98 F fdxA complement(2256082..2256426) Rv2008c compleme 18, 1, 0 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 2, 0 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.81 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 3, 0 121 ccact TGGGGACCATTGACCCTG ttgtc 138 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 20, 1, 0 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.91 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 20, 2, 0 28 tgggc TAGTGACAAACGCCTCCT gagca 45 0.69 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 22, 1, 0 72 aacac TAGGGTCGTTTGACCCGT gggcc 89 0.89 F Rv2626c complement(2952560..2952991) Rv2627c compl 22, 2, 0 238 gatag TGATGCCGATCGGCCCCG atcgg 255 0.73 F Rv2626c complement(2952560..2952991) Rv2627c compl 23, 1, 0 35 cgcgt TAGGGACTTACGTCCCGC cggaa 52 1.00 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 2, 0 104 gttgt GGTGGCCCAAGTGCCCTA aggtg 121 0.62 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 3, 0 274 cagtg AAGTGACGAAAGACCCCA gtgga 291 0.99 F Rv2627c complement(2953505..2954746) Rv2628 295505 24, 1, 0 47 ccggt GGATGACTTTGGTCCCTA tgcct 64 0.95 F Rv2629 2955765..2956889 Rv2628 2955056..2955418 26, 1, 0 432 cattg AGAGGACCAATGACCCTA tttga 449 0.92 F Rv3127 3492144..3493178 Rv3125c complement(3490473 28, 1, 0 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.92 F Rv3130c complement(3494972..3496363) Rv3131 349654 30, 1, 0 74 tctcc CAGGGGCGTTGGTCCCCA cctga 91 0.98 F Rv3134c complement(3499940..3500746) PPE__e290950 30, 2, 0 95 cacct GAGGGCCGTTAGTCCTTA tcgac 112 0.99 F Rv3134c complement(3499940..3500746) PPE__e290950 33 motifs Column 1 : Sequence Number, Site Number Column 2 : Motif type Column 3 : 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 ====================================================================== ======================== MAP MAXIMIZATION RESULTS ==================== ====================================================================== ============================================================= ====== Results by Sequence ===== ============================================================= 1, 1, 0 983 ttggc ATGGGACTTTCGGCCCTG tccgc 1000 0.59 F Rv0079 88202..89023 Rv0078 86526..87131 5UTR ge 2, 1, 1 9 attgg CCGCGGGCGGCCCGCACG catcc 26 0.00 F Rv0081 89573..89917 Rv0080 89020..89478 5UTR ge 3, 1, 1 17 atccg CATGGGGTCGCCCAGCGG gtccc 34 0.22 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 3, 2, 0 41 tcccg AGGGGACTTTTGGCCACC ggcgc 58 0.71 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 3, 3, 0 65 gcgct GGTGGCCTACTGCCCTCC cgccg 82 0.03 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 4, 1, 1 252 ttgcg CCGTCGGTCGACAGGCGA actgc 269 0.00 F Rv0572c complement(665040..665381) Rv0573c complem 5, 1, 1 64 cacgt CATACGATCGGCCGGCGG cggcc 81 0.55 F Rv0574c complement(667250..668392) Rv0575c complem 5, 2, 0 94 gtggg TGGGGCCGAAGGTCCTCA agacc 111 0.99 F Rv0574c complement(667250..668392) Rv0575c complem 5, 3, 1 136 cattg CCGGCGACAAACCGTGCC tacct 153 0.00 F Rv0574c complement(667250..668392) Rv0575c complem 8, 1, 0 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 0.98 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 2, 0 46 ggggc TGGGGACGTCGGTCACGA atggc 63 0.97 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 3, 0 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 9, 1, 0 31 gagcc CGGGGACTTCGGTCCCCA gagcc 48 0.97 F Rv1734c complement(1960772..1961014) Rv1735c compl 10, 1, 0 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 2, 0 132 cccct GGCGGACGAATGACCCCA gtggc 149 0.94 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 3, 0 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 0.94 F narK2 complement(1964181..1965368) Rv1738 1965655. 12, 1, 1 63 acgcg CAGTGGATGCGTCGAAGG gtcaa 80 0.27 F Rv1813c complement(2055679..2056110) Rv1814 205651 12, 2, 0 254 ccggg TAGGGCATAAAGTCTCTA acagc 271 0.70 F Rv1813c complement(2055679..2056110) Rv1814 205651 12, 3, 0 287 ccgga TAGGGAACAACGGCCTTC gggca 304 0.80 F Rv1813c complement(2055679..2056110) Rv1814 205651 13, 1, 0 91 cagcg CTGGACCGTAGGTCCCTG cagtg 108 0.58 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 2, 0 113 gcagt GGATGACTTACGGCCCTG atcca 130 0.93 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 3, 1 167 gccaa CCGTCGGTTGAGCGTCTG gctgc 184 0.61 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 16, 1, 0 53 cggtc ATGAGGCTTTAGTCCCCA atcgg 70 0.54 F Rv2005c complement(2250994..2251881) otsB 2252000. 16, 2, 1 73 ccaat CGGACGGCCAACCGACCA tgatt 90 0.35 F Rv2005c complement(2250994..2251881) otsB 2252000. 16, 3, 1 92 accat GATTGGATTCGACGCCCG aatcc 109 0.21 F Rv2005c complement(2250994..2251881) otsB 2252000. 17, 1, 1 25 cgatg CCGAGGATCGCGCCTATC caaag 42 0.20 F fdxA complement(2256082..2256426) Rv2008c compleme 17, 2, 0 59 accgg AAAGGACCAAAGGCCTTA ttcgt 76 0.98 F fdxA complement(2256082..2256426) Rv2008c compleme 17, 3, 1 124 aaacc GGGGCGGTTCACCCGACC gccag 141 0.24 F fdxA complement(2256082..2256426) Rv2008c compleme 18, 1, 0 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 2, 0 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.81 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 3, 0 121 ccact TGGGGACCATTGACCCTG ttgtc 138 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 20, 1, 0 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.91 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 20, 2, 0 28 tgggc TAGTGACAAACGCCTCCT gagca 45 0.69 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 20, 3, 1 105 ccgag CGGGCGATCAGCCAACGA cagga 122 0.32 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 21, 1, 1 38 tcgtg CCGGCGGATGATCCGAGG tcg 55 0.33 F Rv2625c complement(2951320..2952501) Rv2626c compl 22, 1, 0 72 aacac TAGGGTCGTTTGACCCGT gggcc 89 0.89 F Rv2626c complement(2952560..2952991) Rv2627c compl 22, 2, 1 93 gtggg CCGCGGGTCGATGGACCC gtact 110 0.41 F Rv2626c complement(2952560..2952991) Rv2627c compl 22, 3, 0 238 gatag TGATGCCGATCGGCCCCG atcgg 255 0.73 F Rv2626c complement(2952560..2952991) Rv2627c compl 23, 1, 0 35 cgcgt TAGGGACTTACGTCCCGC cggaa 52 1.00 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 2, 0 104 gttgt GGTGGCCCAAGTGCCCTA aggtg 121 0.62 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 3, 0 274 cagtg AAGTGACGAAAGACCCCA gtgga 291 0.99 F Rv2627c complement(2953505..2954746) Rv2628 295505 24, 1, 0 47 ccggt GGATGACTTTGGTCCCTA tgcct 64 0.95 F Rv2629 2955765..2956889 Rv2628 2955056..2955418 26, 1, 1 331 gcgct CAGCTCATCGACCGCAGC atcga 348 0.36 F Rv3127 3492144..3493178 Rv3125c complement(3490473 26, 2, 1 352 gcatc GAGCCGGTCCAGCGCCGC gacca 369 0.43 F Rv3127 3492144..3493178 Rv3125c complement(3490473 26, 3, 0 432 cattg AGAGGACCAATGACCCTA tttga 449 0.92 F Rv3127 3492144..3493178 Rv3125c complement(3490473 28, 1, 0 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.92 F Rv3130c complement(3494972..3496363) Rv3131 349654 30, 1, 0 74 tctcc CAGGGGCGTTGGTCCCCA cctga 91 0.98 F Rv3134c complement(3499940..3500746) PPE__e290950 30, 2, 0 95 cacct GAGGGCCGTTAGTCCTTA tcgac 112 0.99 F Rv3134c complement(3499940..3500746) PPE__e290950 30, 3, 1 257 aacca GCGGCCGTCCATCGGCTG catat 274 0.48 F Rv3134c complement(3499940..3500746) PPE__e290950 49 motifs Column 1 : Sequence Number, Site Number Column 2 : Motif type Column 3 : 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 ------------------------------------------------------------------------- MOTIF a Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | 21 40 15 21 0.2 2 | 43 9 6 40 0.4 3 | 18 6 3 71 0.6 4 | 3 15 . 81 0.9 5 | 3 . . 96 1.3 6 | 56 6 31 6 0.6 7 | 6 . 93 . 1.2 9 | 40 53 . 6 0.9 10 | 50 37 12 . 0.8 12 | . 3 . 96 1.3 13 | 15 43 12 28 0.2 14 | . . 100 . 1.4 15 | 3 6 90 . 1.1 16 | 3 21 68 6 0.5 17 | . 46 43 9 0.6 18 | 46 12 15 25 0.3 nonsite 19 19 31 30 site 19 18 30 30 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.217 0.396 0.164 0.223 2 | 0.426 0.098 0.074 0.401 3 | 0.188 0.069 0.045 0.699 4 | 0.039 0.158 0.015 0.788 5 | 0.039 0.009 0.015 0.937 6 | 0.545 0.069 0.313 0.074 7 | 0.069 0.009 0.908 0.014 9 | 0.396 0.515 0.015 0.074 10 | 0.485 0.366 0.134 0.014 12 | 0.009 0.039 0.015 0.937 13 | 0.158 0.426 0.134 0.282 14 | 0.009 0.009 0.967 0.014 15 | 0.039 0.069 0.878 0.014 16 | 0.039 0.218 0.670 0.074 17 | 0.009 0.456 0.432 0.104 18 | 0.455 0.128 0.164 0.253 Background probability model 0.191 0.196 0.311 0.302 16 columns Num Motifs: 32 1, 1 983 ttggc ATGGGACTTTCGGCCCTG tccgc 1000 0.59 F Rv0079 88202..89023 Rv0078 86526..87131 5UTR ge 3, 1 41 tcccg AGGGGACTTTTGGCCACC ggcgc 58 0.71 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 3, 2 65 gcgct GGTGGCCTACTGCCCTCC cgccg 82 0.03 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 5, 1 94 gtggg TGGGGCCGAAGGTCCTCA agacc 111 0.99 F Rv0574c complement(667250..668392) Rv0575c complem 8, 1 24 gctcc TAGGGTCGTTCGGCCTTG gggct 41 0.98 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 2 46 ggggc TGGGGACGTCGGTCACGA atggc 63 0.97 F Rv1733c complement(1959853..1960485) Rv1734c compl 8, 3 128 cggat AAGGGACTTTCGCCCCTT cccgc 145 1.00 F Rv1733c complement(1959853..1960485) Rv1734c compl 9, 1 31 gagcc CGGGGACTTCGGTCCCCA gagcc 48 0.97 F Rv1734c complement(1960772..1961014) Rv1735c compl 10, 1 92 tcagt TAGGGCCGGAAGTCCCCA atgtg 109 1.00 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 2 132 cccct GGCGGACGAATGACCCCA gtggc 149 0.94 F narK2 complement(1964181..1965368) Rv1738 1965655. 10, 3 154 agtgg CCGGGACTTCAGGCCCTA tcgga 171 0.94 F narK2 complement(1964181..1965368) Rv1738 1965655. 12, 1 254 ccggg TAGGGCATAAAGTCTCTA acagc 271 0.70 F Rv1813c complement(2055679..2056110) Rv1814 205651 12, 2 287 ccgga TAGGGAACAACGGCCTTC gggca 304 0.80 F Rv1813c complement(2055679..2056110) Rv1814 205651 13, 1 91 cagcg CTGGACCGTAGGTCCCTG cagtg 108 0.58 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 13, 2 113 gcagt GGATGACTTACGGCCCTG atcca 130 0.93 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 16, 1 53 cggtc ATGAGGCTTTAGTCCCCA atcgg 70 0.54 F Rv2005c complement(2250994..2251881) otsB 2252000. 17, 1 59 accgg AAAGGACCAAAGGCCTTA ttcgt 76 0.98 F fdxA complement(2256082..2256426) Rv2008c compleme 18, 1 64 agggc TAGGGACAGAAGTCCCCG aagcg 81 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 2 86 gaagc GCGGGCCATTTGTCCGCG cccgt 103 0.81 F hspX complement(2278496..2278930) Rv2032 2279127.. 18, 3 121 ccact TGGGGACCATTGACCCTG ttgtc 138 1.00 F hspX complement(2278496..2278930) Rv2032 2279127.. 20, 1 6 tccat TGAGGACCTAAGCCCGTT gggct 23 0.91 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 20, 2 28 tgggc TAGTGACAAACGCCTCCT gagca 45 0.69 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 22, 1 72 aacac TAGGGTCGTTTGACCCGT gggcc 89 0.89 F Rv2626c complement(2952560..2952991) Rv2627c compl 22, 2 238 gatag TGATGCCGATCGGCCCCG atcgg 255 0.73 F Rv2626c complement(2952560..2952991) Rv2627c compl 23, 1 35 cgcgt TAGGGACTTACGTCCCGC cggaa 52 1.00 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 2 104 gttgt GGTGGCCCAAGTGCCCTA aggtg 121 0.62 F Rv2627c complement(2953505..2954746) Rv2628 295505 23, 3 274 cagtg AAGTGACGAAAGACCCCA gtgga 291 0.99 F Rv2627c complement(2953505..2954746) Rv2628 295505 24, 1 47 ccggt GGATGACTTTGGTCCCTA tgcct 64 0.95 F Rv2629 2955765..2956889 Rv2628 2955056..2955418 26, 1 432 cattg AGAGGACCAATGACCCTA tttga 449 0.92 F Rv3127 3492144..3493178 Rv3125c complement(3490473 28, 1 76 tgagg CAGGGCCAAAGGTCCTCC gctgg 93 0.92 F Rv3130c complement(3494972..3496363) Rv3131 349654 30, 1 74 tctcc CAGGGGCGTTGGTCCCCA cctga 91 0.98 F Rv3134c complement(3499940..3500746) PPE__e290950 30, 2 95 cacct GAGGGCCGTTAGTCCTTA tcgac 112 0.99 F Rv3134c complement(3499940..3500746) PPE__e290950 ******* ** ******* 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 = -442.20977 Log Fragmentation portion of MAP for motif a = -2.07944 ------------------------------------------------------------------------- MOTIF b Motif model (residue frequency x 100) ____________________________________________ Pos. # a t c g Info _____________________________ 1 | . . 76 23 0.7 2 | 35 . 47 17 0.3 3 | . 17 . 82 0.9 5 | . 5 58 35 0.4 6 | . . 11 88 0.9 7 | 41 . . 58 0.8 8 | 5 76 17 . 1.0 9 | 5 23 58 11 0.3 10 | 17 . 29 52 0.3 11 | 58 . 17 23 0.6 12 | 5 23 52 17 0.2 13 | 5 . 88 5 0.9 14 | 11 . 17 70 0.5 16 | 35 . 58 5 0.6 17 | . 17 35 47 0.2 18 | 17 . 35 47 0.2 nonsite 19 19 31 30 site 15 10 37 36 Motif probability model ____________________________________________ Pos. # a t c g ____________________________________________ 1 | 0.016 0.017 0.726 0.241 2 | 0.339 0.017 0.457 0.187 3 | 0.016 0.178 0.027 0.779 5 | 0.016 0.070 0.565 0.349 6 | 0.016 0.017 0.134 0.833 7 | 0.393 0.017 0.027 0.564 8 | 0.070 0.715 0.188 0.026 9 | 0.070 0.232 0.565 0.134 10 | 0.178 0.017 0.296 0.510 11 | 0.554 0.017 0.188 0.241 12 | 0.070 0.232 0.511 0.187 13 | 0.070 0.017 0.833 0.080 14 | 0.124 0.017 0.188 0.671 16 | 0.339 0.017 0.565 0.080 17 | 0.016 0.178 0.349 0.456 18 | 0.178 0.017 0.349 0.456 Background probability model 0.191 0.196 0.311 0.302 16 columns Num Motifs: 17 2, 1 9 attgg CCGCGGGCGGCCCGCACG catcc 26 0.00 F Rv0081 89573..89917 Rv0080 89020..89478 5UTR ge 3, 1 17 atccg CATGGGGTCGCCCAGCGG gtccc 34 0.22 F Rv0569 661001..661267 Rv0568 659448..660866 5UT 4, 1 252 ttgcg CCGTCGGTCGACAGGCGA actgc 269 0.00 F Rv0572c complement(665040..665381) Rv0573c complem 5, 1 64 cacgt CATACGATCGGCCGGCGG cggcc 81 0.55 F Rv0574c complement(667250..668392) Rv0575c complem 5, 2 136 cattg CCGGCGACAAACCGTGCC tacct 153 0.00 F Rv0574c complement(667250..668392) Rv0575c complem 12, 1 63 acgcg CAGTGGATGCGTCGAAGG gtcaa 80 0.27 F Rv1813c complement(2055679..2056110) Rv1814 205651 13, 1 167 gccaa CCGTCGGTTGAGCGTCTG gctgc 184 0.61 F ctpF 2240157..2242874 Rv1996 2239002..2239955 5 16, 1 73 ccaat CGGACGGCCAACCGACCA tgatt 90 0.35 F Rv2005c complement(2250994..2251881) otsB 2252000. 16, 2 92 accat GATTGGATTCGACGCCCG aatcc 109 0.21 F Rv2005c complement(2250994..2251881) otsB 2252000. 17, 1 25 cgatg CCGAGGATCGCGCCTATC caaag 42 0.20 F fdxA complement(2256082..2256426) Rv2008c compleme 17, 2 124 aaacc GGGGCGGTTCACCCGACC gccag 141 0.24 F fdxA complement(2256082..2256426) Rv2008c compleme 20, 1 105 ccgag CGGGCGATCAGCCAACGA cagga 122 0.32 F Rv2623 2949591..2950484 Rv2622 2948634..2949455 21, 1 38 tcgtg CCGGCGGATGATCCGAGG tcg 55 0.33 F Rv2625c complement(2951320..2952501) Rv2626c compl 22, 1 93 gtggg CCGCGGGTCGATGGACCC gtact 110 0.41 F Rv2626c complement(2952560..2952991) Rv2627c compl 26, 1 331 gcgct CAGCTCATCGACCGCAGC atcga 348 0.36 F Rv3127 3492144..3493178 Rv3125c complement(3490473 26, 2 352 gcatc GAGCCGGTCCAGCGCCGC gacca 369 0.43 F Rv3127 3492144..3493178 Rv3125c complement(3490473 30, 1 257 aacca GCGGCCGTCCATCGGCTG catat 274 0.48 F Rv3134c complement(3499940..3500746) PPE__e290950 *** ********** *** 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 b = -272.61973 Log Fragmentation portion of MAP for motif b = -2.07944 Log Background portion of Map = -11207.51582 Log Alignment portion of Map = -267.33600 Log Site/seq portion of Map = -39.06240 Log Null Map = -12276.71642 Non Palindromic Map = 4.47602 Log Map = 43.81381 log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null Frequency Map = 24.397186 Nearopt Map = 42.732208 Maximal Map = 43.813808 Elapsed time: 335.120000 secs