AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i035_Sugars_Metabolism_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 BIME6 21 BIME #2 araB 300 L-ribulokinase #3 yiaK 200 putative dehydrogenase #4 yiaM 117 orf, hypothetical protein #5 sgaT 291 orf, hypothetical protein #6 HI1024 49 hexulose-6-phosphate synthase, putative #7 HI1027 58 L-xylulose kinase (lyx) #8 HI1028 30 conserved hypothetical protein #9 HI1030 71 conserved hypothetical transmembrane protein #10 HI1031 175 conserved hypothetical protein Motif number 1 TGAAATCAAGTTTCGCATATTGAAATTTTAAGCC 3 144 1 TTTCATATAA 0.75388 -57 TATGACAGACATAGCCTCAAGGAATAGCT 4 99 1 ATACTCAAAA 0.82929 -19 AGTGTCAGGATTAATCAAAACCAATCACATATTG 5 38 0 TTACAAAAAA 0.930091 -254 AAATCTTTCCATACTCAAAATCAACAACAACTTC 5 116 0 ATACAAAAAA 0.939161 -176 GTGTAATTCAATTAACTAAATGAATTTAAATGGA 5 158 1 ATTCTAAAAA 0.914571 -134 ATAGAGTGGGATTCACACAACGAAACAATTATCC 5 189 0 ATTCACAAAA 0.970313 -103 CGCGTCACATTTAATCATAAATAATCTTGTTGTG 5 245 1 TTACATAAAA 0.92574 -47 TCACTCTAATTTTCAAAAGTAATCACAACAAG 5 270 0 ATTCAAAAAA 0.97085 -22 CGTTTTTCCTTAAATAATATGAGGAAG 6 33 0 TTTCTTAAAA 0.902245 -17 ATAGGCTGGATTTTACATAATAAAAATCCAGCCC 7 14 1 TTTCATAAAA 0.965353 -45 ACGAATCACATTTGTGATAATCAATTGGAGGTGT 9 47 1 TTTGATAAAA 0.737274 -25 AATATGAAATATTATCACAAGAAAATAGGATCTA 10 16 1 ATTCACAAAA 0.970306 -160 ACGTTTCATAATTTACAAAAATAAGAAAGCTCAG 10 120 0 ATTCAAAAAA 0.970881 -56 *** ***** ** Masking position 9 Map Score: 13.4863 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 117 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 ATTAAAAGCATTCTGTAACAAAGCGGGACCAA 2 88 1 TTTGTAACAA 0.541731 -213 TCGACAGATAATTTATAACCAATTGATTTTTA 3 58 1 ATTATAACAA 0.887417 -143 TTTTTATGTCTTTTGAAATTCATCAATCAGAT 3 84 1 TTTGAAATCA 0.732128 -117 TGATCGATATATTTGAAATCAAGTTTCGCATA 3 131 1 ATTGAAATAA 0.906416 -70 CAAAAAAGCGATCAAAAAAACAAGGAAGCCTG 3 177 1 ATAAAAAACA 0.648981 -24 CTCTAACTATATTAATAATTCAGGTTGCTGCA 4 53 1 ATAATAATCA 0.788964 -65 ATTTAATGGAATGTGTAATTCAATTAACTAAA 5 146 1 ATTGTAATCA 0.895296 -146 GATTTTTATTATGTAAAATCCAGCCTATTGA 7 10 0 ATTAAAATCA 0.947981 -49 AATCCAGCCCATAAAAAACTAAGGAGAATAT 7 38 1 ATAAAAACAA 0.7984 -21 AAACGCCATAATATAAAACGAATCACATTTGT 9 30 1 ATTAAAACAA 0.925013 -42 TAAATAAATTATTTATAAATCAATATGTTAAA 10 73 0 ATTATAAACA 0.786316 -103 CAGTCAATAAATGTAAAATAAATAAATTATTT 10 91 0 ATTAAAATAA 0.929529 -85 TAATTTTACTATATAAAATTAAGAGAGGAAAA 10 153 1 ATTAAAATAA 0.929529 -23 ** ****** ** Masking position 7 Map Score: 8.26331 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 120 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 AATGTCTGATGCAATATGGAC 2 2 0 GCAATATGGA 0.904345 -299 CGCAGTGACGGCAATGTCTGATGCAATATG 2 14 0 GCAATGTCTG 0.968226 -287 GTGCAAATAATCAATGTGGACTTTTCTGCC 2 160 0 TCAATGTGGA 0.868713 -141 CTATGGCATAGCAAAGTGTGACGCCGTGCA 2 185 0 GCAAAGTGTG 0.969445 -116 TGATGGTAGCGCAAAGTGTGCCGTAGTTCA 3 23 1 GCAAAGTGTG 0.969445 -178 GCTTAAAATTTCAATATGCGAAACTTGATT 3 147 0 TCAATATGCG 0.852299 -54 ATTCCTTGAGGCTATGTCTGTCATAATTCA 4 94 0 GCTATGTCTG 0.794737 -24 TCAATTCGAATCAATATGTGATTGGTTTTG 5 27 1 TCAATATGTG 0.961088 -265 AAGATTTAATGGAATGTGTAATTCAATTAA 5 143 1 GGAATGTGTA 0.830339 -149 CAGCAATATGTTTCCAGTAAAA 9 3 1 GCAATATGTT 0.93894 -69 TATTTATAAATCAATATGTTAAAATAATTT 10 66 0 TCAATATGTT 0.849614 -110 ********** Masking position 4 Map Score: 9.60151 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 515 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 TTGTTACGCGTTTTTGTCATGGCTTTGGTCCCG 2 111 0 TTTTTCAGGC 0.991621 -190 TCCACATTGATTATTTGCACGGCGTCACACTTT 2 170 1 TTATTCAGGC 0.949129 -131 CCATACCCGTTTTTTTGGATGGAGTGAAACG 2 280 1 TTTTTGAGGA 0.967247 -21 TATCGATCACTTTTTAACAAGGCAATCTGATTG 3 107 0 TTTTTCAGGC 0.991621 -94 GGCTTCCTTGTTTTTTTGATCGCTTTTTTGGCT 3 174 0 TTTTTGACGC 0.92904 -27 TGACACTATTTTTTCAGGAAGGCAATGACCATT 5 65 1 TTTTCGAGGC 0.959893 -227 ATTTTTTGACTTTTTGCCAGGGAAGTTGTTGTT 5 95 1 TTTTTCAGGA 0.974867 -197 TTGTTGTTGATTTTGAGTATGGAAAGATTTAAT 5 120 1 TTTTGTAGGA 0.77685 -172 TGTGATTCGTTTTATATTATGGCGTTTTACTGG 9 24 0 TTTATTAGGC 0.863096 -48 ***** ** *** Masking position 9 Map Score: 9.01366 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 137 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 5 CACTGCGTCTTTTACTGGCTCTTCTCGCTAA 2 37 1 TTTACTGCTC 0.922562 -264 CAATGTGGACTTTTCTGCCGTGATTATAGAC 2 148 0 TTTTCTGCGT 0.889803 -153 CCATACCCGTTTTTTTGGATGGAGTGAAACG 2 280 1 TTTTTTGATG 0.708613 -21 ACCAATTGATTTTTATGTCTTTTGAAATTCA 3 75 1 TTTTATGCTT 0.881226 -126 TTTTGATCGCTTTTTTGGCTTAAAATTTCAA 3 163 0 TTTTTTGCTT 0.967819 -38 GCAATGACCATTTTTTGACTTTTTGCCAGGG 5 86 1 TTTTTTGCTT 0.967819 -206 AAGACAGAATTATACTGCCTTCCTCATATTA 6 15 1 TATACTGCTT 0.844914 -35 TCCTTAGTTTTTTATGGGCTGGATTTTTATT 7 32 0 TTTATGGCTG 0.838011 -27 TTAAAATAATTTTACTGATTTTGTGATCTAG 10 47 0 TTTACTGTTT 0.791482 -129 TTATTTTACATTTATTGACTGAGCTTTCTTA 10 102 1 TTTATTGCTG 0.96125 -74 ******* *** Masking position 3 Map Score: 5.1415 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 524 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 6 GTGACGGCAATGTCTGATGCAATATGGAC 2 10 0 TGTCTGATGC 0.83734 -291 GGCATAGCAAAGTGTGACGCCGTGCAAATA 2 181 0 AGTGTGACGC 0.939214 -120 AGGATCCGCTAATCTTATGGATAAAAATGC 2 214 0 AATCTTATGG 0.758432 -87 TTAACAAGGCAATCTGATTGATGAATTTCA 3 97 0 AATCTGATTG 0.925286 -104 ACGCCTGGGTAATGTTATTGCTCTAACTAT 4 33 1 AATGTTATTG 0.825542 -85 TTCGAATCAATATGTGATTGGTTTTGATTA 5 31 1 TATGTGATTG 0.883639 -261 ACATGGATAGAGTGGGATTCACACAACGAA 5 199 0 AGTGGGATTC 0.851556 -93 TTTATGATTAAATGTGACGCGACCCGCAAA 5 236 0 AATGTGACGC 0.949322 -56 GATTATCACAAATGTGATTCGTTTTATATT 9 39 0 AATGTGATTC 0.967497 -33 ********** Masking position 7 Map Score: 3.10531 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 417 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 TTACATACCGGATGCGGCTAC 1 6 0 TCCGGATGCG 0.992168 -16 TAAGCGGGGTTACCGGTTGGGTTAGCGAGAA 2 58 0 TCCGGTTGGG 0.949249 -243 CCCGCTTTGTTACAGAATGCTTTTAATAAGC 2 84 0 TCAGAATGCT 0.834975 -217 TAGCGGATCCTACCTGACGCTTTTTATCGCA 2 233 1 TCCTGACGCT 0.905728 -68 TTGCGCTACCATCAGGACGCGACAAA 3 6 0 ACAGGACGCG 0.952818 -195 ATATTAATAATTCAGGTTGCTGCACATGCGA 4 61 1 TCAGGTTGCT 0.967697 -57 TGGAATTATTTGCGGGTCGCGTCACATTTAA 5 228 1 TCGGGTCGCG 0.977685 -64 * ********* Masking position 3 Map Score: 1.36273 Number of sites scoring better than the average of aligned sites = 1648 Number in coding regions = 1310 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 8 CAAAAAAACAAGGAAGCCTGGG 3 189 1 AGGAAGCCTG 0.991743 -12 CGTCTACGCCAGAACGCCTGGGTAATGTTA 4 20 1 AGAACGCCTG 0.960026 -98 CTATTTTTTCAGGAAGGCAATGACCATTTT 5 70 1 AGGAAGGCAA 0.941397 -222 AAATAATATGAGGAAGGCAGTATAATTCTG 6 19 0 AGGAAGGCAG 0.988211 -31 CCTTGTGTTAAGAAAGTCTGTT 8 3 0 AGAAAGTCTG 0.951328 -28 ********** Masking position 4 Map Score: 1.93637 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 126 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ********** No masking Map Score: -8.14692e-13 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 10 ********** No masking Map Score: -8.14692e-13 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 11 ********** No masking Map Score: -8.14692e-13 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