AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iglpR_ecoli_hinf_100.orf -g0.5 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glpT_glpA 272 glpT: sn-glycerol-3-phosphate permease, glpA: sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit #2 glpG 44 protein of glp regulon #3 glpE_glpD 189 glpE: protein of glp regulon, glpD: sn-glycerol-3-phosphate dehydrogenase (aerobic) #4 glpK 22 glycerol kinase #5 glpF 300 facilitated diffusion of glycerol #6 HI0616 197 ATP-dependent helicase (hepA) #7 HI0618 26 glp protein, putative #8 HI0619 29 glycerol-3-phosphate regulon repressor (glpR) #9 HI0680 31 rarD protein, putative #10 HI0681 300 transcriptional activator (ilvY) #11 HI0685_HI0686 200 HI0685: anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA), HI0686: glycerol-3-phosphatase transporter (glpT) #12 HI0687 99 conserved hypothetical protein #13 HI0688 94 H. influenzae predicted coding region HI0688 #14 HI0690 229 glycerol uptake facilitator protein (glpF) Motif number 1 GGCTAAATGGTAAAAAACGAACTTCAGAGGGAT 1 15 0 TAAAAAGAAT 0.944608 -258 TAGCCATAGTAAAAACATGAATTGTTTGATTTC 1 43 1 AAAAAAGAAT 0.880326 -230 CATTCATAAATTAAATGTGAATTGCCGCACACA 1 155 0 TTAAAGGAAT 0.810912 -118 CGCTTCGACGTAAACTGTGCGGTAAATTTGCCC 3 141 1 TAAACGGCGT 0.803652 -49 TCAGATGGAATAAATGGCGCGATAACGCTCATT 5 138 1 TAAATGGCGT 0.829633 -163 TGCCTCGTCATAAAATGAGCGTTATCGCGCCAT 5 151 0 TAAAAGGCGT 0.967914 -150 GTTAACGAGCAAAAACGAGAAATATCGAACTTA 5 193 0 AAAAAGGAAT 0.958389 -108 AATAATGGTTTAAAATAAGGATTTCTT 9 15 1 TAAAAAGGAT 0.762552 -17 TAAAAAGTGCGGTTAGTTTTCTG 10 1 1 TAAAAGGCGT 0.967914 -300 TTGCCGCCTGAAAAATTGGAAATTTGTAGGAAA 10 103 1 AAAAATGAAT 0.761909 -198 TTATTTCCTGAAAAATTGGAAATTTGCTTAACG 10 174 0 AAAAATGAAT 0.761909 -127 CGATATTAAATAAAAGAAGAAATT 10 287 1 TAAAAAGAAT 0.944608 -14 AAAAAAAATCAAAAATGTGAAGTGTTTCACAAA 11 19 1 AAAAAGGAAT 0.958389 -182 AAAAATAATATAAAAAGTGTAATCATTGTAGGG 11 149 0 TAAAAGGTAT 0.871536 -52 TTAGCTTAAAAAAGGCGGTGGGCAAATTG 12 7 1 TAAAAAGCGT 0.905968 -93 ATAAGAATAATAAAAAGATAAGTATCATTTTTG 12 65 1 TAAAAGTAAT 0.725873 -35 AAACTTAAATGGAGAATTGCTAACGCCC 13 77 0 TAAATGGAAT 0.896041 -18 ***** * *** * Masking position 4 Map Score: 15.0932 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 295 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 2 TCGACGTAAACTGTGCGGTAAATTTGCCCACT 3 145 1 CTGTGCGGAA 0.963951 -45 GAAGGATGAAAAGTGTGGCAAACCGTAATCTG 5 24 0 AAGTGTGGAA 0.981916 -277 ATCTTCCTAAAAGTGCGGTCAATTTTTTGTGA 6 103 1 AAGTGCGGAA 0.997617 -95 TAAAAAGTGCGGTTAGTTTTCTGGTA 10 5 1 AAGTGCGGAG 0.992296 -296 CTTCAATTTAAAGTGCGGGTAAAATTTAGCGT 10 48 0 AAGTGCGGAA 0.997617 -253 CATTGTAGGGAAGTGCGGCCAAAATTAACAAC 11 127 0 AAGTGCGGAA 0.997617 -74 CACTCCTTAGAAGTGCGGTTGAAATGAAGAGT 14 204 0 AAGTGCGGGA 0.992296 -26 ******** ** Masking position 4 Map Score: 14.1698 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 10 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 ATTGTTTGATTTCGCGCATATTCGCTCATA 1 63 1 TTCGCGCATA 0.896405 -210 TTCGCGCATATTCGCTCATAATTCGAAAGT 1 73 1 TTCGCTCATA 0.976329 -200 TGTTAGATCATTCGCGCAACAAATTTATTA 5 90 0 TTCGCGCAAC 0.940627 -211 GTCCGTGACTTTCACGCATACAACAAACAT 5 261 1 TTCACGCATA 0.963841 -40 ATTTACGCATAAGCACGAGAT 7 2 1 TTTACGCATA 0.716502 -25 CTGAACTCGCTACGCTCAAACAGACGAAAA 10 136 0 TACGCTCAAA 0.937685 -165 AATTTTCGCATTCGCTCAAACGGTGTAAAG 11 53 0 TTCGCTCAAA 0.97201 -148 CGCTTTCTTTTACACTCAAAATGTTGTTAA 11 105 1 TACACTCAAA 0.868721 -96 ********** Masking position 8 Map Score: 9.24673 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 197 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 AAACAAGTGGGCAAATTTACCGCACAGTTT 3 152 0 GCAAATTTAC 0.889447 -38 GAAACTCACAAAAAATTGACCGCACTTTTA 6 110 0 AAAAATTGAC 0.685786 -88 AAAATTTCCTACAAATTTCCAATTTTTCAG 10 110 0 ACAAATTTCC 0.96217 -191 TCAAACAGACGAAAATTTCCTACAAATTTC 10 121 0 GAAAATTTCC 0.900922 -180 AGCGAGTTCAGAAAATTTCCGTTAAGCAAA 10 155 1 GAAAATTTCC 0.900922 -146 TTTCCGTTAAGCAAATTTCCAATTTTTCAG 10 170 1 GCAAATTTCC 0.911363 -131 AGGCGACTAAGCAATTTGCCCACCGCCTTT 12 21 0 GCAATTTGCC 0.926472 -79 AAGGGCGTTAGCAATTCTCCATTTAAGTTT 13 75 1 GCAATTCTCC 0.926472 -20 CGTAGAAACTAAAAATCTACTCTAACAGAG 14 63 1 AAAAATCTAC 0.685786 -167 ********** Masking position 6 Map Score: 8.18258 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 458 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 AATTTATGAATGTTTTCTTAACATCGCGGC 1 176 1 TGTTTTCTTA 0.817571 -97 GCGTCTCTCTTTCTTTACAAACAAGT 3 174 0 CTCTTTCTTT 0.908655 -16 AGGGAGCTAATTTATTCTTTCTTCAATTTA 10 70 0 TTTATTCTTT 0.842984 -231 AAGTAGGGCGTGTTTTCTTTTTGCCTACTT 10 211 1 TGTTTTCTTT 0.94754 -90 TTTTTGCCTACTTTTGCTTTGCACGAGCAA 10 228 1 CTTTTGCTTT 0.843878 -73 TGGCGACCTACTTTTTCTTTGCTCGTGCAA 10 246 0 CTTTTTCTTT 0.962851 -55 AATTTCTTCTTTTATTTAATAT 10 289 0 TTTCTTCTTT 0.818594 -12 TTTTTGATTTTTTTTACTTTCTT 11 4 0 TTTTTACTTT 0.731009 -197 ATCACAAAATCGCTTTCTTTTACACTCAAA 11 95 1 CGCTTTCTTT 0.90294 -106 TTTTATATTATTTTTTCTTACATTTTGGGA 11 167 1 TTTTTTCTTA 0.827351 -34 CAAAACACTCCGTATTCTTTTTTAATAAAT 14 149 1 CGTATTCTTT 0.870766 -81 ********** Masking position 5 Map Score: 8.64242 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 199 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 TGTTATCCCTCTGAAGTTCGT 1 1 1 TGTTATCCCC 0.968172 -272 ATGAATTGTTTGATTTCGCGCATATTCGCTC 1 59 1 TGATTTCGCC 0.873811 -214 CATTCACTTTCGTTAAAGCTCATAAATGTTC 3 19 1 CGTTAAAGCC 0.822844 -171 CATAAATGTTCGTTATCGAACATATTAGCAA 3 39 1 CGTTATCGAC 0.915196 -151 ATAAAATGAGCGTTATCGCGCCATTTATTCC 5 144 0 CGTTATCGCC 0.985925 -157 GTAAACTTATCGTTAACGAGCAAAAACGAGA 5 206 0 CGTTAACGAC 0.900809 -95 CAATAATTTTCGCATTCGCTCAAACGGTGTA 11 56 0 CGCATTCGCC 0.763067 -145 TGTTTACCCCCGATTCCCAAA 11 190 0 TGTTTACCCC 0.955637 -11 AATGGAGAATTGCTAACGCCCTTAATAAAAC 13 67 0 TGCTAACGCC 0.949717 -28 ACCGTGGGTATGTTTACCCACGGTTGTGAGG 14 15 0 TGTTTACCCC 0.955637 -215 AAATGAAGAGTGTTTTCCCTAAGTAAAGGGA 14 184 0 TGTTTTCCCA 0.668542 -46 ********* * Masking position 2 Map Score: 7.06732 Number of sites scoring better than the average of aligned sites = 1478 Number in coding regions = 1394 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 7 GCTTATTCCACACAAAAGGGGACAGTATAAAGC 2 12 0 CACAAAGGGC 0.984245 -33 TCTTTCTTTACAAACAAGTGGGCAAATTTACCG 3 160 0 CAAAAAGTGC 0.982974 -30 AAGAAACTCACAAAAAATTGACCGCACTTTTAG 6 109 0 CAAAAATTAC 0.751118 -89 TTTCAGGCGGCAAAGAAGGGAGCTAATTTATTC 10 83 0 CAAAAAGGAC 0.982974 -218 ATGATAGTTACAAAAAAGGCGACTAAGCAATTT 12 34 0 CAAAAAGGGC 0.994181 -66 ACCTAGAATTCAAATAAGGAGGCTATTTCAAAA 14 121 1 CAAAAAGGGC 0.994181 -109 **** **** * * Masking position 7 Map Score: 4.67283 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 42 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 TAAATTAAATGTGAATTGCCGCACACATTATTAAA 1 147 0 GTGATGCACA 0.99226 -126 ACATTTTAGAGTGATATGTATAACATTATGGCGTT 3 99 1 GTGATGAACA 0.9722 -91 CCTTCTCCTGGTGACATAATCCACATCAATCGAAA 5 51 1 GTGATACACA 0.984144 -250 TGTTGCGCGAATGATCTAACAAACATGCATCATGT 5 99 1 ATGATAAACA 0.822033 -202 CGCTCATTTTATGACGAGGCACACACATTTTAAGT 5 163 1 ATGAAGCACA 0.938322 -138 AATCAAAAATGTGAAGTGTTTCACAAATCTTTACA 11 25 1 GTGATGCACA 0.99226 -176 GAAAATTATTGTGATCAATATCACAAAATCGCTTT 11 76 1 GTGAAACACA 0.964288 -125 **** ** **** Masking position 4 Map Score: 4.96473 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 17 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 AATAAGATTTACAAAATGTTCAAAATGACGC 1 118 0 AAAAATGTTC 0.819926 -155 CGTTAAAGCTCATAAATGTTCGTTATCGAAC 3 29 1 CTAAATGTTC 0.879833 -161 CGATTCTTTGCTAATATGTTCGATAACGAAC 3 46 0 CAATATGTTC 0.879834 -144 ACATATCACTCTAAAATGTTTTTTCAATGTT 3 87 0 CAAAATGTTT 0.921198 -103 CAGATAAACGCCATAATGTTATACATATCAC 3 109 0 CATAATGTTA 0.881934 -81 CCACATCAATCGAAAATGTTAATAAATTTGT 5 71 1 CAAAATGTTA 0.979332 -230 TAAAAAAAATCAAAAATGTGAAGTGTTTCAC 11 18 1 CAAAATGTGA 0.926392 -183 CCCCCGATTCCCAAAATGTAAGAAAAAATAA 11 174 0 CAAAATGTAA 0.894645 -27 TTACTTTTCCCAAAAATGATACTTATCTTTT 12 77 0 CAAAATGATA 0.881934 -23 * ********* Masking position 6 Map Score: 4.87284 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 47 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 AATTCATGTTTTTACTATGGCTAAATGGTAAAAAA 1 31 0 TTTATAGAAA 0.860265 -242 CTCTTTCTGATTTACATTGATAAAACTTGGGGGCG 6 166 0 TTTAATGAAA 0.960167 -32 GTCCGTTTAATTTGGATAAAGGATTCGCT 8 6 1 TTTATTGAAA 0.967248 -24 TTACCCGCACTTTAAATTGAAGAAAGAATAAATTA 10 58 1 TTTAATGAAA 0.960167 -243 TTTTACTTTTCCCAAAAATGATACTT 12 84 0 TTTATTTAAA 0.810764 -16 TAACTAGGTTTCTATATCGTAGAAACTAAAAATCT 14 46 1 TCTAATGAAA 0.886714 -184 TTCTCTTCCCTTTACTTAGGGAAAACACTCTTCAT 14 178 1 TTTATTGAAA 0.970564 -52 **** ** * *** Masking position 4 Map Score: 1.24292 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 22 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 CTCATAATTCGAAAGTGAAACGTGATTTCA 1 87 1 GAAAGTGAAA 0.964354 -186 GAGCTTTAACGAAAGTGAATGAGGGCAGC 3 10 0 GAAAGTGAAT 0.964354 -180 TGTTTGTAAAGAAAGAGAGACGC 3 177 1 GAAAGAGAGA 0.892755 -13 ATGTAAATCAGAAAGAGAATAATT 6 184 1 GAAAGAGAAT 0.964354 -14 AAGAAAGTAAAAAAAATCAAAA 11 3 1 GAAAGTAAAA 0.751312 -198 CCGTTTGAGCGAATGCGAAAATTATTGTGA 11 60 1 GAATGCGAAA 0.839582 -141 GAGTGTAAAAGAAAGCGATTTTGTGATATT 11 92 0 GAAAGCGATT 0.85842 -109 CTAAGTAAAGGGAAGAGAATTTATTAAAAA 14 167 0 GGAAGAGAAT 0.877836 -63 ********** Masking position 3 Map Score: 4.28249 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 257 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 ACATTTTGGGAATCGGGGGTAAACA 11 186 1 AATCGGGGGT 0.978926 -15 TATCCCTCACAACCGTGGGTAAACATACCC 14 11 1 AACCGTGGGT 0.986819 -219 AAACCTAGTTAACCGTGGGTATGTTTACCC 14 27 0 AACCGTGGGT 0.986819 -203 ********** Masking position 2 Map Score: 0.77058 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 12 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 TATTTAATAATGTGTGCGGCAATTCACATT 1 145 1 TGTGTGCGGC 0.970232 -128 GCCGTTTCTTGAGTTGCCGCGATGTTAAGA 1 191 0 GAGTTGCCGC 0.92603 -82 TTATGGCGTTTATCTGCCGCTTCGACGTAA 3 124 1 TATCTGCCGC 0.926839 -66 TAATCTGCAAGGCGTGCCGC 5 1 0 GGCGTGCCGC 0.981488 -300 TGCAGATTACGGTTTGCCACACTTTTCATC 5 22 1 GGTTTGCCAC 0.90174 -279 ACTTAAAATGTGTGTGCCTCGTCATAAAAT 5 168 0 TGTGTGCCTC 0.922778 -133 TTAGCTCCCTTCTTTGCCGCCTGAAAAATT 10 90 1 TCTTTGCCGC 0.926838 -211 TCATTGTAGGGAAGTGCGGCCAAAATTAAC 11 130 0 GAAGTGCGGC 0.86059 -71 ********** Masking position 5 Map Score: 1.48712 Number of sites scoring better than the average of aligned sites = 1439 Number in coding regions = 1361 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 14 CCCCTTTTGTGTGGAATAAGCGACAGCAAC 2 24 1 GTGGAATAAG 0.98065 -21 TTCGATTGATGTGGATTATGTCACCAGGAG 5 55 0 GTGGATTATG 0.966376 -246 TCCCTATACGGTGGATTTAGTCGAGATTCT 6 17 1 GTGGATTTAG 0.952511 -181 GATGATGTTGGTGGAATAGGTATAGTTAAA 13 22 1 GTGGAATAGG 0.977063 -73 ********** Masking position 5 Map Score: 0.116725 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 26 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 ********** No masking Map Score: 3.98858e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0