AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_Glycolysis_+_PPS_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 asnS 168 asparagine tRNA synthetase #2 pncB 265 nicotinate phosphoribosyltransferase #3 glk 203 glucokinase #4 pgi 300 glucosephosphate isomerase #5 HI0556 85 oxidoreductase, putative (devB) #6 HI0557 82 H. influenzae predicted coding region HI0557 #7 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #8 HI0559 194 sulfite synthesis pathway protein (cysQ) #9 HI0559.1 56 H. influenzae predicted coding region HI0559.1 #10 HI0561 300 conserved hypothetical protein #11 HI1302 147 asparaginyl-tRNA synthetase (asnS) #12 HI1573 300 pyruvate kinase, type II (pykA) #13 HI1574 33 replicative DNA helicase (dnaB) #14 HI1576 54 glucose-6-phosphate isomerase (pgi) Motif number 1 ACCAGACTCTATAAAAGATGCTAAAGGTTATTT 2 8 0 ATAAAATAAG 0.892321 -258 GGTGTATGTTATAAAAATGTAGCAATAAAGGCGTTT 2 103 0 ATAAAAGAAT 0.794655 -163 CCTGTTTTTGATAAAACTGTTGCAAATGCTTACCTG 8 137 0 ATAAAAGAAA 0.923387 -58 CTATTAAAGAATAAAATTTTTAATAACAGTTCATTA 10 45 0 ATAAAAATAA 0.780956 -256 TTTTCATTTAATAAAAATCCTATTAAAGAATAAAAT 10 64 0 ATAAAAATAA 0.765287 -237 TGAAAAAAAAATAAAAACAGGTTAATTTAAACATTT 10 94 1 ATAAAATAAT 0.839537 -207 TTTTTTTAACATAAAATTTGTTTTATTGAAAAATGT 10 124 0 ATAAAATTAT 0.471996 -177 AAATTTTATGTTAAAAAAACTTGAAAAATAGTCAAA 10 141 1 TTAAAATAAA 0.850716 -160 TGAGTCCTAAATAAAATAGGGTAAAGCCTTATTAAT 11 30 0 ATAAAATAAG 0.892321 -118 GTTATGAACAATAAAATCGCCTTAAAAATGAGTCCT 11 58 0 ATAAAATAAA 0.942196 -90 ATAAAATTGCCGATAGTTTACCTTAA 11 132 0 ATAAAAGTAG 0.788325 -16 TGTGTTCAAGTTAAAAATATCTATAATCACGACTAC 12 93 0 TTAAAATTAA 0.777656 -208 AGTATTTTTCTTAAAACCCGATATAACTGGCAAAAA 12 129 1 TTAAAATTAA 0.777656 -172 AAAAAAGTAAACAAAACCAGCTTAAATAACTGAGCC 12 160 1 ACAAAATAAA 0.675506 -141 CATTATACGCTTAAAACTTTTGGAAATCAAAAACGG 12 194 0 TTAAAAGAAA 0.808421 -107 ATTCTCCCTAATAAAAATTCCAGAAA 14 39 1 ATAAAAAAAA 0.85372 -16 ****** * *** Masking position 6 Map Score: 9.65474 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 146 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 TTATAAATAAAGGGTGAGCGGGGCGGTTGT 4 95 1 AGGGTGAGCG 0.959912 -206 ATCTGCATTTTTGGTGGGGTGATGATCGT 5 67 1 TTGGTGGGGT 0.93263 -19 AATCTAATGTAGGGTGGGCTTTAGCCACGC 6 13 1 AGGGTGGGCT 0.989856 -70 AACATAATAAATTGTGGGCTAAAGCCCACC 6 50 1 ATTGTGGGCT 0.872939 -33 GATTTTCCGTAGGGTGGGCTTTAGCCCACA 6 62 0 AGGGTGGGCT 0.989856 -21 ATTTTTGACAAGGTTGCGCGGTTTTCTTTT 10 176 1 AGGTTGCGCG 0.879424 -125 AAATATAGTGTTGGTGCGGGTTATGAACAA 11 83 0 TTGGTGCGGG 0.902586 -65 CCACCTTGACATGGTGGGGGTCACTGGTTC 12 26 0 ATGGTGGGGG 0.983601 -275 ********** Masking position 5 Map Score: 7.68766 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 277 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 ATAACATACACCGCGTAATGCCATCGACCA 2 127 1 CCGCGTAATG 0.988214 -139 GTATCTGACCCCGCATAAGGAATAGAAC 3 9 0 CCGCATAAGG 0.99303 -195 TTAATTTGTTCCGCATAAGGTGATTTGGCT 5 29 0 CCGCATAAGG 0.99303 -57 TATTCGGCTTCCGAGTAATGTCGAAAATAA 7 46 0 CCGAGTAATG 0.973834 -30 TACTCGGAAGCCGAATAAGGAATAATT 7 59 1 CCGAATAAGG 0.986011 -17 ********** Masking position 6 Map Score: 7.29919 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 6 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 CCGAAATCTTTCGCTGCATTTGCGAATTCT 1 54 1 TCGCTGCATT 0.992114 -115 AACGCCTTTATTGCTACATTTTTATAACAT 2 104 1 TTGCTACATT 0.708324 -162 CAAAAAGGCATCGCTGCAATTGGTGCTGAA 3 56 1 TCGCTGCAAT 0.963122 -148 AATAAATGCTTCACTGCGCTAAGGGTTTAC 4 180 1 TCACTGCGCT 0.845078 -121 GGAATTATCCTCGGTGCATTGATTACGGTA 10 263 1 TCGGTGCATT 0.974566 -38 ACGGTAATTTTCACTGCATCCAAT 10 287 1 TCACTGCATC 0.926934 -14 AGATAAAAAATCGGTGCACATTATACGCTT 12 218 0 TCGGTGCACA 0.888184 -83 TTATTTTACTTCGCTACATATTAGCCAGAT 12 244 0 TCGCTACATA 0.90068 -57 TCACTGCATTTTTTGAACAG 14 1 1 TCACTGCATT 0.97632 -54 ********** Masking position 5 Map Score: 6.60001 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 462 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 AGGCGTTTGTACCTGAAAAGATGAAGATTCT 2 80 0 ACTGAAAAGA 0.905871 -186 TAGTTTGCCCAGCTTGCAAAAAGGCATCGCT 3 40 1 ACTTGCAAAA 0.905871 -164 GGAACAAATTAACTGGAAAAATCTGCATTTT 5 47 1 ACTGGAAAAA 0.962046 -39 GATTTTTATTAAATGAAAAAAAAATAAAAAC 10 81 1 AATGAAAAAA 0.658718 -220 ATGTTAAAAAAACTTGAAAAATAGTCAAATT 10 148 1 ACTTGAAAAA 0.951663 -153 TTGTTCCTTGAGCTTAAAAAAAGAAAACCGC 10 193 0 ACTTAAAAAA 0.938622 -108 GTATAACGAAAACTTAAAAGAATTGACCGTT 10 229 1 ACTTAAAAGA 0.882007 -72 AACCCGATATAACTGGCAAAAAAGTAAACAA 12 143 1 ACTGGCAAAA 0.925317 -158 AAACAAAACCAGCTTAAATAACTGAGCCGTT 12 168 1 ACTTAAATAA 0.706808 -133 * ********* Masking position 4 Map Score: 4.9109 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 263 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 GAATTATTTTGACTTTAGCGGAGCAGTTGA 3 181 1 GACTTTAGCG 0.919665 -23 TCTTCTGGCCTGCGCTAGCGCAGGTAGTAC 4 63 1 TGCGCTAGCG 0.922782 -238 CACTCAACATTACGCTAACGGCACTAAAAC 4 209 1 TACGCTAACG 0.793201 -92 ATGTAGGGTGGGCTTTAGCCACGCTCTTAC 6 19 1 GGCTTTAGCC 0.902706 -64 CCGTAGGGTGGGCTTTAGCCCACAATTTAT 6 56 0 GGCTTTAGCC 0.902706 -27 ATTTTATGCTGACGCTAACGAACATTTACT 8 78 1 GACGCTAACG 0.92128 -117 ATATTAATAAGGCTTTACCCTATTTTATTT 11 28 1 GGCTTTACCC 0.886488 -120 CGACTAGCTGGACTCGAACCAGTGACCCCC 12 11 1 GACTCGAACC 0.799816 -290 GTCAAGGTGGTGCTCTAACCAACTGAGCTA 12 46 1 TGCTCTAACC 0.918484 -255 ********** Masking position 7 Map Score: 4.31215 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 662 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 TGGGGTCATGCGGATTTTTCATCCACTCCT 4 131 1 CGGATTTTTC 0.961456 -170 CTAAAACCATCACATTTTTCTGTGACTGGC 4 232 1 CACATTTTTC 0.940701 -69 ACCAAAAATGCAGATTTTTCCAGTTAATTT 5 52 0 CAGATTTTTC 0.958519 -34 TTCTGGATAGCCTATTTTTCACT 9 44 1 CCTATTTTTC 0.958519 -13 GGTTAATTTAAACATTTTTCAATAAAACAA 10 113 1 AACATTTTTC 0.861129 -188 CAAAAATTTGACTATTTTTCAAGTTTTTTT 10 153 0 ACTATTTTTC 0.900323 -148 CTTGAACACAAGTATTTTTCTTAAAACCCG 12 119 1 AGTATTTTTC 0.861129 -182 ATAATGTGCACCGATTTTTTATCTGGCTAA 12 224 1 CCGATTTTTT 0.802273 -77 ********** Masking position 4 Map Score: 4.49085 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 206 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 GGGAGCCGATTAGCTCCCTGATGATA 1 1 0 TGCCCTGAAA 0.901273 -168 AATATTCTCTCTGTTAATAGTCGGAAAAA 1 150 0 ATCCCTGTAA 0.991755 -19 CTGTTGCGTAAATCGCGCTATGCAGAATCTTCATCT 2 57 1 ATCCCTATAA 0.964929 -209 CCGGAAAGGCAGGCTCCCTGTAAATATCGATCTGGG 3 106 0 AGCCCTGTAA 0.985532 -98 AATAATTCTTTCTCACACTGTAAATACCTGGGGGCA 3 153 0 TTCCCTGTAA 0.977796 -51 ACTGAGCTATAGTCGCACTGTGTGAAGTAGTCGTGA 12 67 1 ATCCCTGTGA 0.969651 -234 AGGGAGAATGACTCCCTCTGTTCAAAAAATGCAGTG 14 12 0 ATCCCTGTAA 0.991755 -43 AGAGGGAGTCATTCTCCCTAATAAAAATTCCAGAAA 14 29 1 ATCCCTAAAA 0.909686 -26 * ** * **** * * Masking position 16 Map Score: 6.88253 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 23 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 9 AATTAAAGGTAAAAAAAGGGAGCCGATTAGCTCC 1 20 0 AAAAAAGACC 0.983075 -149 TATTCTAGAGAAAAAAACCAATCGAACCAA 7 7 0 AAAAAAAACG 0.955379 -69 ATTAAATGAAAAAAAAATAAAAACAGGTTAATTT 10 88 1 AAAAAAAAAC 0.784847 -213 CCTTGAGCTTAAAAAAAGAAAACCGCGCAACCTT 10 185 0 AAAAAAAACC 0.965663 -116 ACGAAAACTTAAAAGAATTGACCGTTTGAGGAAT 10 234 1 AAAAAAGACG 0.977887 -67 AAAACCAGCTTAAATAACTGAGCCGTTTTTGATT 12 172 1 TAAAAAGACC 0.923423 -129 TAAATATGTTAAAATAAAAGAGCG 13 20 1 AAAAAAGACG 0.977887 -14 **** ** ** ** Masking position 7 Map Score: 2.69204 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 31 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 CCGCTCACCCTTTATTTATAAATGTACTACC 4 85 0 TTTATTATAA 0.712113 -216 GTTATTATTTAAAACCCTAGCCAA 5 4 1 ATTATTAAAA 0.583824 -82 TTGCAACAGTTTTATCAAAAACAGGTTCATG 8 148 1 TTTATCAAAA 0.683733 -47 CTAATGAACTGTTATTAAAAATTTTATTCTT 10 44 1 GTTATTAAAA 0.847815 -257 TTTTTTTTCATTTAATAAAAATCCTATTAAA 10 73 0 TTTAATAAAA 0.818946 -228 ATAAAAACAGGTTAATTTAAACATTTTTCAA 10 104 1 GTTAATTAAA 0.452327 -197 TAAAATTTGTTTTATTGAAAAATGTTTAAAT 10 118 0 TTTATTAAAA 0.908737 -183 TAAAACAAATTTTATGTTAAAAAAACTTGAA 10 135 1 TTTATGTAAA 0.646027 -166 GTTTTCTTTTTTTAAGCTCAAGGAACAATTT 10 196 1 TTTAAGTCAA 0.476164 -105 CAAGGAACAATTTATGTATAACGAAAACTTA 10 214 1 TTTATGATAA 0.798175 -87 GTTGGTGCGGGTTATGAACAATAAAATCGCC 11 73 0 GTTATGACAA 0.773955 -75 ACACTATATTTTTATGGAAAATTTCCTTCAT 11 102 1 TTTATGAAAA 0.940315 -46 TATATCGGGTTTTAAGAAAAATACTTGTGTT 12 123 0 TTTAAGAAAA 0.861519 -178 ****** **** Masking position 4 Map Score: 4.28295 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 239 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 11 TAACATAGGTATCCCCCCATTTACGGGTGG 1 108 1 ATCCCCCCAT 0.982195 -61 ATCACACCATATGCCACCTTTCTGGTCGAT 2 149 0 ATGCCACCTT 0.920765 -117 TTGAACCCCGATCACACCATATGCCACCTT 2 159 0 ATCACACCAT 0.956748 -107 CGTTGTTGTTATGCCCCCAGGTATTTACAG 3 142 1 ATGCCCCCAG 0.952768 -62 AAAAATCCGCATGACCCCATCGTTGACAAC 4 120 0 ATGACCCCAT 0.97848 -181 ACGATCATCACCCCACCAAAAATGCA 5 70 0 ATCACCCCAC 0.943522 -16 GCGAAGTAAAATAACACCTTTAAAATTTTG 12 260 1 ATAACACCTT 0.707789 -41 ********** Masking position 1 Map Score: 3.2735 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 149 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 ATTTTTATAACATACACCGCGTAATGCCAT 2 121 1 CATACACCGC 0.821029 -145 GGGGGCATAACAACAACGCCGGAAAGGCAG 3 130 0 CAACAACGCC 0.961525 -74 TCTTCAACTGCTCCGCTAAAGTCA 3 190 0 CAACTGCTCC 0.808892 -14 CCATCGTTGACAACCGCCCCGCTCACCCTT 4 104 0 CAACCGCCCC 0.971564 -197 GCGGATTTTTCATCCACTCCTGGCGGTCAG 4 140 1 CATCCACTCC 0.934554 -161 TTTTTGGCAGCAACCACGGCATTACAAATA 8 38 0 CAACCACGGC 0.98255 -157 TTTTGGAAATCAAAAACGGCTCAGTTATTT 12 183 0 CAAAAACGGC 0.838457 -118 ********** Masking position 2 Map Score: 0.709356 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 919 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 13 ********** No masking Map Score: -2.0084e-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 14 ********** No masking Map Score: -2.0084e-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: -2.0084e-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