AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iglpR_ecoli_hinf_300.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 292 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 TTACGGTTTGCCACACTTTTCATCCTTCTC 5 28 1 CCACACTTTT 0.974678 -273 AAAAAATTGACCGCACTTTTAGGAAGATAT 6 101 0 CCGCACTTTT 0.99491 -97 AGAAAACTAACCGCACTTTTTA 10 3 0 CCGCACTTTT 0.99491 -298 TAAATTTTACCCGCACTTTAAATTGAAGAA 10 52 1 CCGCACTTTA 0.972246 -249 GTGAAACACTTCACATTTTTGATTTTTTTT 11 111 0 TCACATTTTT 0.712982 -182 TTAATTTTGGCCGCACTTCCCTACAATGAT 11 223 1 CCGCACTTCC 0.96209 -70 AATTTGCCCACCGCCTTTTTTAAGCTAA 12 9 0 CCGCCTTTTT 0.969055 -91 AATTGCTTAGTCGCCTTTTTTGTAACTATC 12 35 1 TCGCCTTTTT 0.86046 -65 TTCATTTCAACCGCACTTCTAAGGAGTGAT 14 208 1 CCGCACTTCT 0.989643 -22 ********** Masking position 7 Map Score: 13.8336 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 229 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 TGTTTTTACTATGGCTAAATGGTAAAAAACGAACTTCA 1 22 0 ATGTAAAAAA 0.932933 -251 GCACACATTATTAAATAAGATTTACAAAATGTTCAAAA 1 124 0 TTATAAAAAA 0.806146 -149 GCCGCGATGTTAAGAAAACATTCATAAATTAAATGTGA 1 168 0 TAGAAAAAAA 0.806261 -105 CTCATTCACTTTCGTTAAAGCTCATAAATGTTCGTTAT 3 17 1 TTGTAAAAAA 0.884929 -173 GAATCGCGCTTTAGGTAACATTGAAAAAACATTTTAGA 3 71 1 TTGTAAAAAA 0.885853 -119 TGCCCACTTGTTTGTAAAGAAAGAGAGACGC 3 169 1 TTGAAAAAGA 0.807657 -21 ATCCACATCAATCGAAAATGTTAATAAATTTGTTGCGC 5 69 1 ATGAAAAAAA 0.969611 -232 CTGTAAACTTATCGTTAACGAGCAAAAACGAGAAATAT 5 201 0 ATGTAAAAAA 0.932933 -100 CATACTCTTGAAAAGAAACTCACAAAAAATTGACCGCA 6 116 0 AAAAAAAAAA 0.805221 -82 TTTAGCGTATTTTGAAAAATACCAGAAAACTAACCGCA 10 18 0 TTGAAAAAAA 0.947346 -283 CGCCTGAAAAATTGGAAATTTGTAGGAAATTTTCGTCT 10 107 1 ATGAAAAGAA 0.882715 -194 GAAACCCGATATTAAATAAAAGAAGAAATT 10 281 1 ATAATAAAAA 0.589407 -20 ATGACACATAATTAAAAAGTTGGAGAAAAAATT 11 6 0 ATAAAAAAAA 0.947013 -287 GGATTTGCGAATCATAAAAGAAAATAAAAAATAAGAAA 11 71 1 ATAAAAAAAA 0.946988 -222 AAAATAAAAAATAAGAAAGTAAAAAAAATCAAAAATGT 11 91 1 ATAAAAAAAA 0.947013 -202 CCCAAAATGTAAGAAAAAATAATATAAAAAGTGTAATC 11 250 0 AAAAAAAAAA 0.805221 -43 AAGAGAATTTATTAAAAAAGAATACGGAGTGTTTTGAA 14 147 0 ATAAAAAGGA 0.493288 -83 ** * *** * *** Masking position 8 Map Score: 14.705 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 247 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 TTAAATGTGAATTGCCGCACACATTATTAA 1 148 0 ATTGCCGCAC 0.958981 -125 AGTGGGCAAATTTACCGCACAGTTTACGTC 3 147 0 TTTACCGCAC 0.98939 -43 CAGATTACGGTTTGCCACACTTTTCATCCT 5 24 1 TTTGCCACAC 0.926336 -277 TCACAAAAAATTGACCGCACTTTTAGGAAG 6 105 0 TTGACCGCAC 0.990163 -93 TACCAGAAAACTAACCGCACTTTTTA 10 7 0 CTAACCGCAC 0.966323 -294 ACGCTAAATTTTACCCGCACTTTAAATTGA 10 48 1 TTACCCGCAC 0.976748 -253 GTTGTTAATTTTGGCCGCACTTCCCTACAA 11 219 1 TTGGCCGCAC 0.99184 -74 ACTCTTCATTTCAACCGCACTTCTAAGGAG 14 204 1 TCAACCGCAC 0.961193 -26 ********** Masking position 9 Map Score: 11.8329 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 155 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TATGAGCGAATATGCGCGAAATCAAACAAT 1 63 0 TATGCGCGAA 0.900897 -210 ACTTTCGAATTATGAGCGAATATGCGCGAA 1 73 0 TATGAGCGAA 0.974892 -200 TAATAAATTTGTTGCGCGAATGATCTAACA 5 90 1 GTTGCGCGAA 0.937789 -211 ATGTTTGTTGTATGCGTGAAAGTCACGGAC 5 261 0 TATGCGTGAA 0.961477 -40 ATCTCGTGCTTATGCGTAAAT 7 2 0 TATGCGTAAA 0.706259 -25 TTTTCGTCTGTTTGAGCGTAGCGAGTTCAG 10 136 1 TTTGAGCGTA 0.934069 -165 CTTTACACCGTTTGAGCGAATGCGAAAATT 11 145 1 TTTGAGCGAA 0.970889 -148 TTAACAACATTTTGAGTGTAAAAGAAAGCG 11 197 0 TTTGAGTGTA 0.859866 -96 ********** Masking position 10 Map Score: 8.86789 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 5 CTGTGCGGTAAATTTGCCCACTTGTTTGTAA 3 155 1 ATTTGCCCAC 0.987709 -35 AATACGCTAAATTTTACCCGCACTTTAAATT 10 45 1 ATTTACCCGC 0.963021 -256 TTAGCTCCCTTCTTTGCCGCCTGAAAAATTG 10 90 1 TTTTGCCGCC 0.927578 -211 GCGTGTTTTCTTTTTGCCTACTTTTGCTTTG 10 218 1 TTTTGCCTAC 0.912463 -83 AATGTTGTTAATTTTGGCCGCACTTCCCTAC 11 216 1 ATTTGGCCGC 0.916851 -77 TGTTTACCCCCGATTCCCAAA 11 282 0 TTTTACCCCC 0.963021 -11 GCGACTAAGCAATTTGCCCACCGCCTTTTTT 12 18 0 ATTTGCCCAC 0.987709 -82 ACCGTGGGTATGTTTACCCACGGTTGTGAGG 14 15 0 TTTTACCCAC 0.969148 -215 * ********* Masking position 5 Map Score: 7.22598 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 279 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 TTTAGCCATAGTAAAAACATGAATTGTTTGATT 1 41 1 GAAAACTGAA 0.621915 -232 CCACACAAAAGGGGACAGTATAAAGCG 2 5 0 GGACAGATAA 0.713609 -40 TCGTTAACGAGCAAAAACGAGAAATATCGAACT 5 195 0 GAAAACAGAA 0.928294 -106 ATATACTCAAGCGTAAACTAGAATCTCGACTAA 6 33 0 GGAAACAGAA 0.945572 -165 ACTTTAAATTGAAGAAAGAATAAATTAGCTCCC 10 66 1 GAAAAGATAA 0.907915 -235 GCAAAAGTAGGCAAAAAGAAAACACGCCCTACT 10 212 0 GAAAAGAAAC 0.835307 -89 TTCTTTGCTCGTGCAAAGCAAAAGTAGGCAAAA 10 229 0 GGAAAGAAAA 0.973077 -72 TGCTTTGCACGAGCAAAGAAAAAGTAGGTCGCC 10 242 1 GGAAAGAAAA 0.973077 -59 AAATAAAAAATAAGAAAGTAAAAAAAATCAAAA 11 92 1 TAAAAGAAAA 0.679702 -201 TATCATTTTTGGGAAAAGTAAAA 12 87 1 GGAAAGAAAA 0.973077 -13 TTTCTATATCGTAGAAACTAAAAATCTACTCTA 14 54 1 GAAAACAAAA 0.940102 -176 * * **** **** Masking position 7 Map Score: 6.98527 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 147 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 CATCGCGGCAACTCAAGAAACGGCAGGTTCTCTCA 1 197 1 ACTAAAAGGA 0.936073 -76 GTCGCTTATTCCACACAAAAGGGGACAGTATAAAG 2 13 0 CCAAAAAGGA 0.98462 -32 CTCTTTCTTTACAAACAAGTGGGCAAATTTACCGC 3 159 0 ACAAAGTGGA 0.79547 -31 GTGACATAATCCACATCAATCGAAAATGTTAATAA 5 61 1 CCAAAATGAA 0.877287 -240 AATCCTTTATCCAAATTAAACGGAC 8 1 0 CCAAAAAGGC 0.944457 -29 TTCTTTGCCGCCTGAAAAATTGGAAATTTGTAGGA 10 99 1 CCTAAATGGA 0.98462 -202 TGCCTTATTTCCTGAAAAATTGGAAATTTGCTTAA 10 176 0 CCTAAATGGA 0.98462 -125 GAGTGTTTTCCCTAAGTAAAGGGAAGAGAATTTAT 14 173 0 CCTAAAAGGA 0.98462 -57 *** * *** ** * Masking position 8 Map Score: 3.58327 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 96 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 ACATATTAGCAAAGAATCGCGCTTTAGGTAACATT 3 58 1 AAAAACCTTT 0.876412 -132 TGTATGCGTGAAAGTCACGGACCTCCACGATGCTT 5 248 0 AAATCCCCTC 0.882553 -53 AACTCACAAAAAATTGACCGCACTTTTAGGAAGAT 6 103 0 AAATGCACTT 0.723008 -95 AAGAAATCCTTATTTTAAACCATTA 9 17 0 AAGAACATTT 0.533539 -15 AAATACCAGAAAACTAACCGCACTTTTTA 10 5 0 AAATACACTT 0.877764 -296 GTATTTTTCAAAATACGCTAAATTTTACCCGCACT 10 34 1 AAAACCATTT 0.945862 -267 AAGAAAGAATAAATTAGCTCCCTTCTTTGCCGCCT 10 77 1 AAATACCTTC 0.767746 -224 GGCAAAAAGAAAACACGCCCTACTTTGCCTTATTT 10 201 0 AAAACCACTT 0.947396 -100 AAGATTTGTGAAACACTTCACATTTTTGATTTTTT 11 113 0 AAAACTATTT 0.547503 -180 TCAATATCACAAAATCGCTTTCTTTTACACTCAAA 11 182 1 AAATCCCTTT 0.944025 -111 AGTGCGGCCAAAATTAACAACATTTTGAGTGTAAA 11 205 0 AAATACATTT 0.887376 -88 GGCTATTTCAAAACACTCCGTATTCTTTTTTAATA 14 141 1 AAAACCATTC 0.901266 -89 CTTTTTTAATAAATTCTCTTCCCTTTACTTAGGGA 14 165 1 AAATCCCCTT 0.942012 -65 TACTTAGGGAAAACACTCTTCATTTCAACCGCACT 14 190 1 AAAACCATTT 0.951949 -40 *** ** * **** Masking position 2 Map Score: 9.28398 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 233 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 9 ATTTCATGCGTCATTTTGAACATTTTGTAA 1 111 1 TCATTTTGAA 0.769864 -162 CATTGAAAAAACATTTTAGAGTGATATGTA 3 89 1 ACATTTTAGA 0.925231 -101 AAATTTATTAACATTTTCGATTGATGTGGA 5 70 0 ACATTTTCGA 0.847898 -231 GCGATAACGCTCATTTTATGACGAGGCACA 5 156 1 TCATTTTATG 0.719813 -145 CGAGGCACACACATTTTAAGTTCGATATTT 5 177 1 ACATTTTAAG 0.904793 -124 GAAACACTTCACATTTTTGATTTTTTTTAC 11 109 0 ACATTTTTGA 0.868978 -184 AAAATTAACAACATTTTGAGTGTAAAAGAA 11 201 0 ACATTTTGAG 0.919848 -92 AAAAGTGTAATCATTGTAGGGAAGTGCGGC 11 232 0 TCATTGTAGG 0.805088 -61 ATTTTTTCTTACATTTTGGGAATCGGGGGT 11 268 1 ACATTTTGGG 0.972235 -25 AAGATAAGTATCATTTTTGGGAAAAGTAAA 12 79 1 TCATTTTTGG 0.913907 -21 ********** Masking position 5 Map Score: 5.3931 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 83 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 TGAAATCACGTTTCACTTTCGAATTATGAG 1 87 0 TTTCACTTTC 0.965588 -186 GCTGCCCTCATTCACTTTCGTTAAAGCTC 3 10 1 ATTCACTTTC 0.965588 -180 GCGTCTCTCTTTCTTTACAAACA 3 177 0 TCTCTCTTTC 0.8962 -13 AATTATTCTCTTTCTGATTTACAT 6 184 0 ATTCTCTTTC 0.965588 -14 TTTTGATTTTTTTTACTTTCTTATTTTTTA 11 95 0 TTTTACTTTC 0.758069 -198 TCACAATAATTTTCGCATTCGCTCAAACGG 11 152 0 TTTCGCATTC 0.844437 -141 AATATCACAAAATCGCTTTCTTTTACACTC 11 184 1 AATCGCTTTC 0.862798 -109 TTTTTAATAAATTCTCTTCCCTTTACTTAG 14 167 1 ATTCTCTTCC 0.881696 -63 ********** Masking position 3 Map Score: 3.90365 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 11 AAACTGTGCGGTAAATTTGCCCACTTGTTT 3 152 1 GTAAATTTGC 0.844111 -38 CTGAAAAATTGGAAATTTGTAGGAAATTTT 10 110 1 GGAAATTTGT 0.923002 -191 GAAATTTGTAGGAAATTTTCGTCTGTTTGA 10 121 1 GGAAATTTTC 0.878062 -180 TTTGCTTAACGGAAATTTTCTGAACTCGCT 10 155 0 GGAAATTTTC 0.878062 -146 CTGAAAAATTGGAAATTTGCTTAACGGAAA 10 170 0 GGAAATTTGC 0.901991 -131 AAAGGCGGTGGGCAAATTGCTTAGTCGCCT 12 21 1 GGCAAATTGC 0.927582 -79 AAACTTAAATGGAGAATTGCTAACGCCCTT 13 75 0 GGAGAATTGC 0.927582 -20 ********** Masking position 5 Map Score: 7.64039 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 145 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 TGTTTACCCCCGATTCCCAAAATGT 11 278 0 ACCCCCGATT 0.977434 -15 GGGTATGTTTACCCACGGTTGTGAGGGATA 14 11 0 ACCCACGGTT 0.986804 -219 GGGTAAACATACCCACGGTTAACTAGGTTT 14 27 1 ACCCACGGTT 0.986804 -203 ********** Masking position 1 Map Score: 0.628549 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 ATTAACAGCCTGATTCAGTGAGAGAACCTGCCGT 1 216 0 TATCGTAGAG 0.988706 -57 TTTATCAATGTAAATCAGAAAGAGAATAATT 6 177 1 TATCGAAGAG 0.955747 -21 GTAGGAAATTTTCGTCTGTTTGAGCGTAGCGAGT 10 128 1 TCTCGTTGAG 0.944923 -173 TTTACCCTTTTGAAACAGTAAGGGATTTGCGAAT 11 49 1 TAACGTAGGG 0.944923 -244 TCACAAATCTTTACACCGTTTGAGCGAATGCGAA 11 137 1 TAACGTTGAG 0.961756 -156 GATTATGATGTTACTCTGTTAGAGTAGATTTTTA 14 72 0 TATCGTAGAG 0.988706 -158 * * ** ** **** Masking position 1 Map Score: 0.598748 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 ********** No masking Map Score: -5.39059e-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 Motif number 15 ********** No masking Map Score: -5.39059e-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