AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_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 ATAACATACACCGCGTAATGCCATCGACCA 2 127 1 CCGCGTAATG 0.989448 -139 GTATCTGACCCCGCATAAGGAATAGAAC 3 9 0 CCGCATAAGG 0.993475 -195 TTAATTTGTTCCGCATAAGGTGATTTGGCT 5 29 0 CCGCATAAGG 0.993475 -57 TATTCGGCTTCCGAGTAATGTCGAAAATAA 7 46 0 CCGAGTAATG 0.976539 -30 TACTCGGAAGCCGAATAAGGAATAATT 7 59 1 CCGAATAAGG 0.987188 -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 2 AAATAACCTTTAGCATCTTTTATAGAGTCTGGT 2 8 1 CTTATTTTAT 0.905918 -258 AAACGCCTTTATTGCTACATTTTTATAACATACACC 2 103 1 ATTCTTTTAT 0.818069 -163 CAGGTAAGCATTTGCAACAGTTTTATCAAAAACAGG 8 137 1 TTTCTTTTAT 0.933352 -58 TAATGAACTGTTATTAAAAATTTTATTCTTTAATAG 10 45 1 TTATTTTTAT 0.80546 -256 ATTTTATTCTTTAATAGGATTTTTATTAAATGAAAA 10 64 1 TTATTTTTAT 0.786807 -237 AAATGTTTAAATTAACCTGTTTTTATTTTTTTTTCA 10 94 0 ATTATTTTAT 0.858463 -207 TTTTTTTAACATAAAATTTGTTTTATTGAAAAATGT 10 124 0 ATAATTTTAT 0.477819 -177 TTTGACTATTTTTCAAGTTTTTTTAACATAAAATTT 10 141 0 TTTATTTTAA 0.868482 -160 ATTAATAAGGCTTTACCCTATTTTATTTAGGACTCA 11 30 1 CTTATTTTAT 0.905918 -118 AGGACTCATTTTTAAGGCGATTTTATTGTTCATAAC 11 58 1 TTTATTTTAT 0.949734 -90 TTAAGGTAAACTATCGGCAATTTTAT 11 132 1 CTACTTTTAT 0.81229 -16 GTAGTCGTGATTATAGATATTTTTAACTTGAACACA 12 93 1 TTAATTTTAA 0.802248 -208 TTTTTGCCAGTTATATCGGGTTTTAAGAAAAATACT 12 129 0 TTAATTTTAA 0.802248 -172 GGCTCAGTTATTTAAGCTGGTTTTGTTTACTTTTTT 12 160 0 TTTATTTTGT 0.707504 -141 CCGTTTTTGATTTCCAAAAGTTTTAAGCGTATAATG 12 194 1 TTTCTTTTAA 0.830595 -107 TTTCTGGAATTTTTATTAGGGAGAAT 14 39 0 TTTTTTTTAT 0.871489 -16 *** * ****** Masking position 11 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 3 GCAGGCCAGAAGAGGCGCGTTGCCCAAGTAACGGT 4 41 0 AGGGGCGTCC 0.991728 -260 ATAAAGGGTGAGCGGGGCGGTTGTCAACGATGGGG 4 101 1 AGGGGCGTTC 0.986943 -200 CTGCATTTTTGGTGGGGTGATGATCGT 5 69 1 GGGGGTGTTC 0.95574 -17 ATCTAATGTAGGGTGGGCTTTAGCCACGCTCTTAC 6 14 1 GGTGGCTTCC 0.991859 -69 ATTTTCCGTAGGGTGGGCTTTAGCCCACAATTTAT 6 56 0 GGTGGCTTCC 0.991859 -27 TTTTTGACAAGGTTGCGCGGTTTTCTTTTTTTAAG 10 177 1 GGTGGCGTTC 0.991864 -124 ACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA 12 41 1 GGGGGCTTCC 0.994851 -260 TGCTCTAACCAACTGAGCTATAGTCGCACTGTGTG 12 56 1 AATGGCTTTC 0.770377 -245 ** ** *** * ** Masking position 11 Map Score: 8.74145 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 284 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 ACAACCGCCCCGCTCACCCTTTATTTATAA 4 95 0 CGCTCACCCT 0.96336 -206 ACGATCATCACCCCACCAAAAATGCAGAT 5 67 0 ACCCCACCAA 0.938273 -19 GCGTGGCTAAAGCCCACCCTACATTAGATT 6 13 0 AGCCCACCCT 0.990753 -70 GGTGGGCTTTAGCCCACAATTTATTATGTT 6 50 0 AGCCCACAAT 0.882955 -33 TGTGGGCTAAAGCCCACCCTACGGAAAATC 6 62 1 AGCCCACCCT 0.990753 -21 AAAAGAAAACCGCGCAACCTTGTCAAAAAT 10 176 0 CGCGCAACCT 0.888993 -125 TTGTTCATAACCCGCACCAACACTATATTT 11 83 1 CCCGCACCAA 0.910504 -65 GAACCAGTGACCCCCACCATGTCAAGGTGG 12 26 1 CCCCCACCAT 0.985043 -275 ********** Masking position 6 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 5 AGAATTCGCAAATGCAGCGAAAGATTTCGG 1 54 0 AATGCAGCGA 0.991956 -115 ATGTTATAAAAATGTAGCAATAAAGGCGTT 2 104 0 AATGTAGCAA 0.704199 -162 TTCAGCACCAATTGCAGCGATGCCTTTTTG 3 56 0 ATTGCAGCGA 0.96241 -148 GTAAACCCTTAGCGCAGTGAAGCATTTATT 4 180 0 AGCGCAGTGA 0.842457 -121 TACCGTAATCAATGCACCGAGGATAATTCC 10 263 0 AATGCACCGA 0.974068 -38 ATTGGATGCAGTGAAAATTACCGT 10 287 0 GATGCAGTGA 0.925576 -14 AAGCGTATAATGTGCACCGATTTTTTATCT 12 218 1 TGTGCACCGA 0.886194 -83 ATCTGGCTAATATGTAGCGAAGTAAAATAA 12 244 1 TATGTAGCGA 0.898887 -57 CTGTTCAAAAAATGCAGTGA 14 1 0 AATGCAGTGA 0.975856 -54 ********** Masking position 6 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 6 CAGAATCTTCATCTTTTCAGGTACAAACGC 2 79 1 ATCTTTTCAG 0.740492 -187 CAGCGATGCCTTTTTGCAAGCTGGGCAAAC 3 42 0 TTTTTGCAAG 0.90468 -162 AAAAATGCAGATTTTTCCAGTTAATTTGTT 5 49 0 ATTTTTCCAG 0.906611 -37 TATTCTCTTGTTTTTGGCAGCAACCACGGC 8 48 0 TTTTTGGCAG 0.678829 -147 GCGTGTTGTCTTCTTTCAATTCAACATGAA 8 173 0 TTCTTTCAAT 0.675355 -22 TGTTTTTATTTTTTTTTCATTTAATAAAAA 10 83 0 TTTTTTTCAT 0.693848 -218 TAATTTAAACATTTTTCAATAAAACAAATT 10 116 1 ATTTTTCAAT 0.72995 -185 AAATTTGACTATTTTTCAAGTTTTTTTAAC 10 150 0 ATTTTTCAAG 0.893395 -151 CGCGGTTTTCTTTTTTTAAGCTCAAGGAAC 10 192 1 TTTTTTTAAG 0.858472 -109 AAACGGTCAATTCTTTTAAGTTTTCGTTAT 10 231 0 TTCTTTTAAG 0.772264 -70 TTTGTTTACTTTTTTGCCAGTTATATCGGG 12 145 0 TTTTTGCCAG 0.916627 -156 CACCTTTAAAATTTTGTAATTATTGACGGA 12 274 1 ATTTTGTAAT 0.538988 -27 ********** Masking position 9 Map Score: 4.9054 Number of sites scoring better than the average of aligned sites = 1038 Number in coding regions = 909 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 7 TGGGGTCATGCGGATTTTTCATCCACTCCT 4 131 1 CGGATTTTTC 0.956697 -170 CTAAAACCATCACATTTTTCTGTGACTGGC 4 232 1 CACATTTTTC 0.933556 -69 ACCAAAAATGCAGATTTTTCCAGTTAATTT 5 52 0 CAGATTTTTC 0.953414 -34 TTCTGGATAGCCTATTTTTCACT 9 44 1 CCTATTTTTC 0.953415 -13 GGTTAATTTAAACATTTTTCAATAAAACAA 10 113 1 AACATTTTTC 0.845966 -188 CAAAAATTTGACTATTTTTCAAGTTTTTTT 10 153 0 ACTATTTTTC 0.888887 -148 CTTGAACACAAGTATTTTTCTTAAAACCCG 12 119 1 AGTATTTTTC 0.845966 -182 ATAATGTGCACCGATTTTTTATCTGGCTAA 12 224 1 CCGATTTTTT 0.782308 -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 GAGCCGATTAGCTCCCTGATGATA 1 1 0 GCCCTGAATA 0.939803 -168 AATATTCTCTCTGTTAATAGTCGGAAAAA 1 150 0 TCCCTGTATA 0.986896 -19 GTTGCGTAAATCGCGCTATGCAGAATCTTCATCT 2 59 1 TCCCTATAGA 0.885834 -207 GGAAAGGCAGGCTCCCTGTAAATATCGATCTGGG 3 106 0 GCCCTGTATA 0.977088 -98 TAATTCTTTCTCACACTGTAAATACCTGGGGGCA 3 153 0 TCCCTGTATA 0.986896 -51 TGAGCTATAGTCGCACTGTGTGAAGTAGTCGTGA 12 69 1 TCCCTGTGAA 0.938882 -232 GGAGAATGACTCCCTCTGTTCAAAAAATGCAGTG 14 12 0 TCCCTGTAAA 0.983004 -43 AGGGAGTCATTCTCCCTAATAAAAATTCCAGAAA 14 31 1 TCCCTAAAAA 0.828848 -24 ** * **** *** Masking position 14 Map Score: 5.11199 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 50 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 TCTTTCGCTGCATTTGCGAATTCTGCTTGT 1 60 1 CATTTGCGAA 0.846912 -109 AAATAACCTTTAGCATCTTTTATAGAG 2 8 1 CTTTAGCATC 0.924087 -258 CAGTCTATTCCTGTTGCGTAAATCGCGCTA 2 47 1 CTGTTGCGTA 0.819322 -219 AGGTGCGCAGTAGCGTCCTCGTACAGG 2 249 0 CAGTAGCGTC 0.941074 -17 ATTATTTTGACTTTAGCGGAGCAGTTGAAG 3 183 1 CTTTAGCGGA 0.87755 -21 GTTTTAGTGCCGTTAGCGTAATGTTGAGTG 4 209 0 CGTTAGCGTA 0.950761 -92 GTAGGGTGGGCTTTAGCCACGCTCTTACTA 6 21 1 CTTTAGCCAC 0.789279 -62 AGTAAATGTTCGTTAGCGTCAGCATAAAAT 8 78 0 CGTTAGCGTC 0.968546 -117 ATCAGGTAAGCATTTGCAACAGTTTTATCA 8 135 1 CATTTGCAAC 0.743022 -60 AATAACAGTTCATTAGCATACTTTGTGGTA 10 30 0 CATTAGCATA 0.88417 -271 ********** Masking position 4 Map Score: 3.9655 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 572 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 10 CCACCCGTAAATGGGGGGATACCTATGTTA 1 108 0 ATGGGGGGAT 0.980782 -61 ATCGACCAGAAAGGTGGCATATGGTGTGAT 2 149 1 AAGGTGGCAT 0.914896 -117 AAGGTGGCATATGGTGTGATCGGGGTTCAA 2 159 1 ATGGTGTGAT 0.953409 -107 CTGTAAATACCTGGGGGCATAACAACAACG 3 142 0 CTGGGGGCAT 0.949139 -62 GTTGTCAACGATGGGGTCATGCGGATTTTT 4 120 1 ATGGGGTCAT 0.976793 -181 TGCATTTTTGGTGGGGTGATGATCGT 5 70 1 GTGGGGTGAT 0.939227 -16 CAAAATTTTAAAGGTGTTATTTTACTTCGC 12 260 0 AAGGTGTTAT 0.691429 -41 ********** Masking position 9 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 11 AGCTAATCGGCTCCCTTTTTTTACCTTTAATTCCG 1 22 1 CCCTTTTTAC 0.985219 -147 TACCTTGTTTCGCAATTTATTGAACCCCGATCACA 2 173 0 CCATTTTTAC 0.971367 -93 ATCTGGGTCACACAATTACTTTATCGTTTCAGCAC 3 78 0 CCATTATTAC 0.971367 -126 GCTCCTCCAACACCGTTACTTGGGCAACGCGCCTC 4 30 1 CCCTTATTGC 0.932887 -271 CCGCCCCGCTCACCCTTTATTTATAAATGTACTAC 4 86 0 CCCTTTTTAA 0.853442 -215 GACGCTAACGAACATTTACTTAACCAAGTATTGCT 8 88 1 ACATTATTAC 0.747725 -107 TCAAAAACGGCTCAGTTATTTAAGCTGGTTTTGTT 12 169 0 CCATTATTAC 0.971367 -132 GTATAATGTGCACCGATTTTTTATCTGGCTAATAT 12 222 1 CCCATTTTAC 0.903648 -79 CGCTCTTTTATTTTAACATATTTAGAT 13 17 0 CCTTTATTAC 0.911593 -17 TCACTGCATTTTTTGAACAGAGGGAGTC 14 4 1 CGCTTTTTAC 0.896166 -51 * ** *** ** * * Masking position 7 Map Score: 7.37411 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 106 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 TGGACAAGTGTTTATTTTTTCCGACTATTA 1 135 1 TTTATTTTTT 0.929127 -34 AGGCGTGTTGTCTTCTTTCAATTCAACA 8 177 0 TGTCTTCTTT 0.87758 -18 TATTAAAAATTTTATTCTTTAATAGGATTT 10 56 1 TTTATTCTTT 0.898185 -245 TTAACCTGTTTTTATTTTTTTTTCATTTAA 10 89 0 TTTATTTTTT 0.929127 -212 GTTGCGCGGTTTTCTTTTTTTAAGCTCAAG 10 188 1 TTTCTTTTTT 0.940587 -113 CTGGTTTTGTTTACTTTTTTGCCAGTTATA 12 150 0 TTACTTTTTT 0.796154 -151 TCACTGCATTTTTTGAACAGAGGG 14 5 1 TGCATTTTTT 0.763349 -50 ********** Masking position 5 Map Score: 1.10526 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 86 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 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 GTATCCCCCCATTTACGGGTGGACAAGTGTTTATTT 1 116 1 ATTACGTGAA 0.978326 -53 TTTTCCGACTATTAACAGAGAGAATATT 1 151 1 ATTACGGGAA 0.99257 -18 CCAGATCGATATTTACAGGGAGCCTGCCTTTCCGGC 3 107 1 ATTACGGGCG 0.946977 -97 GCCCCCAGGTATTTACAGTGTGAGAAAGAATTATTT 3 154 1 ATTACGGGAA 0.99257 -50 ACTTAAAAGAATTGACCGTTTGAGGAATTATCCTCG 10 240 1 ATTACGTGAA 0.978326 -61 TTTTGTAATTATTGACGGAGTAAATA 12 285 1 ATTACGGAAA 0.953844 -16 *** ** * * ** * Masking position 5 Map Score: 1.10091 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 24 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432