AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igalR_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 galE 260 UDP-galactose-4-epimerase #2 mglA 60 ATP-binding component of methyl-galactoside transport and galactose taxis #3 mglB 279 galactose-binding transport protein; receptor for galactose taxis #4 galS 141 mgl repressor, galactose operon inducer #5 galR 300 repressor of galETK operon #6 galP 300 galactose-proton symport of transport system #7 HI0351 172 UDP-glucose 4-epimerase (galE) #8 HI0819 37 galactokinase (galK) #9 HI0820_HI0821 200 HI0820: galactose-1-phosphate uridylyltransferase (galT), HI0821: galactose operon repressor (galR) #10 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #11 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) Motif number 1 GGAATAAATTAGTGGAATCGTTTACACAAGAATTT 1 169 0 ATGAAGTTAC 0.994893 -92 GTTAAGATACTGTGAAATCACTCACAGATTGAAAG 3 14 0 TTGAAATCAC 0.792938 -266 GAGTCACAGCAATGGAAACGGTTACAGCCGTTTTG 4 33 0 ATGAAGTTAC 0.994893 -109 ACACTGAAAGAATGTAAGCGTTTACCCACTAAGGT 5 270 1 ATGAAGTTAC 0.994893 -31 TATCATCACAACTGAAACCGATTACACCAACCACA 6 20 1 ATGAAGTTAC 0.994893 -281 GATAAATGTTAGTGTAAGCGATTACACTGATGTGA 6 202 1 ATGAAGTTAC 0.994893 -99 TTTACGATAAATTGAAAGCGGTTACTTTCATAAGT 9 54 1 ATGAAGTTAC 0.994893 -147 TTTCTTATTTTGTGACAAAGATCACGGTTTATTTA 9 119 1 TTGCAGTCAC 0.949118 -82 AGTATAAATTAATGTAATCGTTTACATTGATAAAA 9 163 1 ATGAAGTTAC 0.994893 -38 TTTGTGACATGGATCACAAATTCATAA 10 3 1 TTGCAGTCAC 0.949118 -88 AATTTGCAAAAATGAAAATGATTACATAAAAAATT 10 36 0 ATGAAGTTAC 0.994893 -55 * ** ** * **** Masking position 7 Map Score: 28.5059 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 17 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 GAATGATTGCGCTTTTTATCTGAAAAAAGA 1 92 0 GCTTTTTATC 0.878762 -169 GAATTTAGCCGTTTTTTATGCGCGATTAAG 1 145 0 GTTTTTTATG 0.96848 -116 AGATGCGCAGGTTTTTTTTGCCGG 5 5 0 GTTTTTTTTG 0.79609 -296 CAATATGGTTATTTTTTATTGTGAATTAAG 6 272 0 ATTTTTTATT 0.899496 -29 CTACAACAATACTTTTTAGCAACAGGTTTT 7 71 1 ACTTTTTAGC 0.674579 -102 TTAGCAACAGGTTTTTTATTTTATTGAAAA 7 86 1 GTTTTTTATT 0.923139 -87 TAGTGATATAATTTTTTAGTCTCAATAATT 7 138 1 ATTTTTTAGT 0.774518 -35 TTTATCGTAAATTATTTATGATCAAAATAT 9 35 0 ATTATTTATG 0.744195 -166 AATAAGCAAAATTTTTTATGATTTAGTTCA 9 90 0 ATTTTTTATG 0.958152 -111 TTTGACTCCTGTTTTTTATCAATGTAAACG 9 181 0 GTTTTTTATC 0.949713 -20 CAAATTCATAATTTTTTATGTAATCATTTT 10 27 1 ATTTTTTATG 0.958152 -64 ********** Masking position 5 Map Score: 10.2251 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 114 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 3 TGGAATAAATTAGTGGAATCGTTTACACAA 1 175 0 TAGTGGAATC 0.792501 -86 AACGTTAAAACGGTGCAATCATAGCTATCA 3 53 0 CGGTGCAATC 0.945104 -227 ACCGTTTTAACGTTGTAACCCGTATGTAAC 3 69 1 CGTTGTAACC 0.887436 -211 GTTGTTATGACGCTGTTACCTCGGCAAAAG 3 111 0 CGCTGTTACC 0.814214 -169 TTAACAAAACGGCTGTAACCGTTTCCATTG 4 29 1 GGCTGTAACC 0.842502 -113 AGCAGTCATTTACTGCAATCTCATAACAGG 4 114 1 TACTGCAATC 0.803679 -28 CTGCGCAGGCTGGTGTAATTCATGTGCTCA 5 33 1 TGGTGTAATT 0.741466 -268 GCGTTTCGCAAAGTGTAACCAAAGGTTTGC 5 150 1 AAGTGTAACC 0.745385 -151 CTGTTGTGGTTGGTGTAATCGGTTTCAGTT 6 29 0 TGGTGTAATC 0.979215 -272 ATAGATTAAACGCTGTTATCTGCAATTAAG 6 128 0 CGCTGTTATC 0.856494 -173 AGATAAATGTTAGTGTAAGCGATTACACTG 6 201 1 TAGTGTAAGC 0.822689 -100 CAAATCACATCAGTGTAATCGCTTACACTA 6 211 0 CAGTGTAATC 0.962646 -90 TAGTATAAATTAATGTAATCGTTTACATTG 9 162 1 TAATGTAATC 0.713009 -39 CATCAATTTTTGTTGTAATCTAAGGGGAAG 11 16 1 TGTTGTAATC 0.902653 -50 ********** Masking position 8 Map Score: 8.92508 Number of sites scoring better than the average of aligned sites = 859 Number in coding regions = 802 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 AATCGTTTACACAAGAATTTAGCCGTTTTTT 1 158 0 ACAAAATTTA 0.973933 -103 CAGCGTCATAACAACAATTAAAGCCGTTTTC 3 126 1 ACAAAATTAA 0.942156 -154 TAAGTGCATGAAAATAATTGAGTTATATCAT 6 159 0 AAAAAATTGA 0.821653 -142 TTTTTTAGTCTCAATAATTAACAAGGAAATC 7 149 1 TCAAAATTAA 0.831561 -24 ATTTTGATCATAAATAATTTACGATAAATTG 9 37 1 TAAAAATTTA 0.65403 -164 CGGTTTATTTACAATAATTTAGTATAAATTA 9 143 1 ACAAAATTTA 0.972302 -58 GTAAACGATTACATTAATTTATACTAAATTA 9 157 0 ACATAATTTA 0.855087 -44 TAGATTAATTACGATAATTTATTT 10 77 1 ACGAAATTTA 0.897374 -14 TTAGATTACAACAAAAATTGATGGGAAA 11 8 0 ACAAAATTGA 0.961546 -58 **** ****** Masking position 6 Map Score: 6.54809 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 32 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 AAAAGTGTGACATGGAATAAATTAGTGGAA 1 187 0 CATGGAATAA 0.966208 -74 ATGAAATAACCATAGCATAACAAAGATGCG 1 217 0 CATAGCATAA 0.966208 -44 ATGGTTATTTCATACCATAAGCCTAATGGA 1 234 1 CATACCATAA 0.923461 -27 CCTTGTTGGCCATACAATAAGGGCGCAGTA 2 32 0 CATACAATAA 0.947174 -29 CGTTACCGGGCATGGAAGAACGAATTTTAA 3 162 1 CATGGAAGAA 0.897938 -118 GTTATATCATCATAGATTAAACGCTGTTAT 6 139 0 CATAGATTAA 0.948678 -162 CAAATTTGCTCATAGATTAATTACGATAAT 10 65 1 CATAGATTAA 0.948678 -26 ********** Masking position 2 Map Score: 5.32882 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 21 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ACTTTTCGCATCTTTGTTATGCTATGGTTA 1 211 1 TCTTTGTTAT 0.953927 -50 AACGGTGCAATCATAGCTATCACATTGTTA 3 45 0 TCATAGCTAT 0.862709 -235 TCTTTTTTTGTCTTACTTATTTGCGTTTGG 5 184 1 TCTTACTTAT 0.879882 -117 CTAACATTTATCTTAGTTATGATTTAAGTG 6 184 0 TCTTAGTTAT 0.953927 -117 AATGATTTCCTTGTTAATTATTGAGAC 7 156 0 TCCTTGTTAA 0.862709 -17 CCCTCTTTGCTAAAGCTAAAGAG 8 25 0 TCTTTGCTAA 0.811039 -13 TCCTTGTTATAATCTATAAA 9 1 1 TCCTTGTTAT 0.944949 -200 ATGATTTAGTTCATACTTATGAAAGTAACC 9 73 0 TCATACTTAT 0.796996 -128 ********** Masking position 9 Map Score: 3.70024 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 54 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 CTTATGCAGGGTAGTGCTTGAGATAAATGCT 3 243 0 GTAGTGTTGA 0.949322 -37 TTGACCGCTGGTGGCGTTTGGCTTCAGGTTG 5 111 0 GTGGCGTTGG 0.986535 -190 GCGAAACGCTGTTGCGATTGACCGCTGGTGG 5 128 0 GTTGCGTTGA 0.987568 -173 GTCTTACTTATTTGCGTTTGGCTCACATTCC 5 193 1 TTTGCGTTGG 0.950796 -108 ATCTTTGTCTGTTGTGGTTGGTGTAATCGGT 6 36 0 GTTGTGTTGG 0.976855 -265 AAGTATTGTTGTAGCGAGTGAGATAACCTCT 7 54 0 GTAGCGGTGA 0.952986 -119 ****** **** Masking position 9 Map Score: 2.81047 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 146 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 ATCTGAAAAAAGACGCGGTTTCATGCCTGC 1 75 0 AGACGCGGTT 0.972673 -186 ATTGTTGTTATGACGCTGTTACCTCGGCAA 3 114 0 TGACGCTGTT 0.937664 -166 ACACTTTGCGAAACGCTGTTGCGATTGACC 5 136 0 AAACGCTGTT 0.959916 -165 ATCATAGATTAAACGCTGTTATCTGCAATT 6 131 0 AAACGCTGTT 0.959916 -170 AATAAAATAAAAAACCTGTTGCTAAAAAGT 7 81 0 AAAACCTGTT 0.821598 -92 ACGATAAATTGAAAGCGGTTACTTTCATAA 9 57 1 GAAAGCGGTT 0.879041 -144 ********** Masking position 3 Map Score: 2.81353 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 230 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 CGGCAAGGTCAGCACTACCGAC 1 3 0 AGCACTACCG 0.852174 -258 ACAGTGAATAATCACTTTTGCCGAGGTAAC 3 97 1 ATCACTTTTG 0.799361 -183 CGATCTGGATCACATTCGTTAACAAAAC 4 9 1 ATCACATTCG 0.908142 -133 CTCTGGGATCACCACTTTAGCAACCTGAAG 5 91 1 ACCACTTTAG 0.833391 -210 CCAGCGGTCAATCGCAACAGCGTTTCGCAA 5 131 1 ATCGCAACAG 0.890146 -170 GCAGATTATCATCACAACTGAAACCGATTA 6 14 1 ATCACAACTG 0.942366 -287 GATTACACCAACCACAACAGACAAAGATTT 6 39 1 ACCACAACAG 0.953551 -262 TGTGAAGCAAATCACATCAGTGTAATCGCT 6 218 0 ATCACATCAG 0.968262 -83 ********** Masking position 1 Map Score: 1.48147 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 435 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 CTAAGGCCGCCTCCGGCAAGGTCAGCACTAC 1 15 0 CCCGGCAAGG 0.962512 -246 TTAGCACCCTCTCCGGCCAACGGTTCGACGC 1 42 1 CCCGGCCAAC 0.982999 -219 CCCGGTAACGCTCCAGAAAACGGCTTTAATT 3 141 0 CCCAGAAAAC 0.797987 -139 AACTCTACTGCCCCGCCGAGCATTTATCTCA 3 225 1 CCCGCCGAGC 0.970302 -55 TTATCTCAAGCACTACCCTGCATAAGAAAAA 3 248 1 CCTACCCTGC 0.806939 -32 ACAAAATAGCCGCCAGCAAGCAGTCATTTAC 4 96 1 CCCAGCAAGC 0.991122 -46 ACATGAATTACACCAGCCTGCGCAGATGCGC 5 27 0 CCCAGCCTGC 0.987074 -274 * ********* Masking position 3 Map Score: 1.04712 Number of sites scoring better than the average of aligned sites = 1668 Number in coding regions = 1610 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 11 ********** No masking Map Score: 6.10599e-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 12 GCGCAATCATTCATAAACCCTCTGTTTTATA 1 110 1 TCAAAACCCT 0.887263 -151 GCTTCGGCGTTCAGTAACACTTCATTAACTC 3 199 1 TCATAACACT 0.974326 -81 CAGTAACACTTCATTAACTCTACTGCCCCGC 3 210 1 TCATAACTCT 0.981943 -70 ATTCACTACCTGTTATGAGATTG 4 129 0 TCATACCTGT 0.911798 -13 ACTTCACCTATCAATACCTCTGGGATCACCA 5 74 1 TCATACCTCT 0.978302 -227 ACGGGCGTTTTCCGTAACACTGAAAGAATGT 5 254 1 TCCTAACACT 0.932786 -47 *** ******* Masking position 6 Map Score: 0.432288 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 48 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 AACCATAGCATAACAAAGATGCGAAAAGTGTG 1 208 0 TAAAAGATGC 0.639035 -53 TCACAGTATCTTAACAATGTGATAGCTATGAT 3 34 1 TTACATGTGA 0.666127 -246 GGTTACAACGTTAAAACGGTGCAATCATAGCT 3 57 0 TTAAAGGTGC 0.899495 -223 GAACGAATTTTAAAAAGTGAGCTTCGGCGTTC 3 179 1 TAAAATGAGC 0.8425 -101 GCCGTTTTGTTAACGAATGTGATCCAGATCG 4 10 0 TAAGATGTGA 0.90207 -132 AAAAGAAATGTAACAACTGTGAAAACCGAATA 6 87 0 TAAAATGTGA 0.949311 -214 TATTGTGAATTAAGATAGGTGAGTACGACGTA 6 254 0 TAAATGGTGA 0.820081 -47 TTTTGTGTGGTAAGAATGGTGATTTTCAATAA 7 106 0 TAAAAGGTGA 0.972823 -67 ATTTCCTTGTTAATTATTGAGACTAAAAAATT 7 147 0 TAATATGAGA 0.604827 -26 TTGCTAAAGCTAAAGAGGGAGACTGACTATA 8 10 0 TAAGAGGAGA 0.888146 -28 TCCAACCTCTTTAAAAAGGGGAAGATCCACTT 11 43 0 TTAAAGGGGA 0.791464 -23 *** ** ***** Masking position 3 Map Score: 1.50152 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 295 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 14 ********** No masking Map Score: 6.10599e-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 CCTCTCCGGCCAACGGTTCGACGCATGCAG 1 49 1 CAACGGTTCG 0.809781 -212 TTTATCTGAAAAAAGACGCGGTTTCATGCC 1 78 0 AAAAGACGCG 0.791715 -183 CATAGCATAACAAAGATGCGAAAAGTGTGA 1 207 0 CAAAGATGCG 0.981681 -54 CACCAGCCTGCGCAGATGCGCAGGTTTTTT 5 18 0 CGCAGATGCG 0.894464 -283 AAAGTGTAACCAAAGGTTTGCAATCTCTTT 5 159 1 CAAAGGTTTG 0.882039 -142 CCACAACAGACAAAGATTTGTAATATTTTC 6 50 1 CAAAGATTTG 0.923171 -251 TAAGCGATTACACTGATGTGATTTGCTTCA 6 216 1 CACTGATGTG 0.821731 -85 GTACGACGTAAAAAGATGTGAAGCAAATCA 6 234 0 AAAAGATGTG 0.900018 -67 ********** Masking position 5 Map Score: 0.19106 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 582 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331