AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_ecoli_hinf_reg_100.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 aroL 182 shikimate kinase II #2 serC 198 3-phosphoserine aminotransferase #3 aroA 70 5-enolpyruvylshikimate-3-phosphate synthetase #4 b1691 220 putative amino acid/amine transport protein #5 aroD 30 3-dehydroquinate dehydratase #6 aroC 34 chorismate synthase #7 yrdD 62 putative DNA topoisomerase #8 smf_2 53 orf, fragment 2 #9 smf_1 129 orf, fragment 1 #10 aroB 56 3-dehydroquinate synthase #11 aroK 199 shikimate kinase I #12 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #13 HI0207 284 shikimic acid kinase I (aroK) #14 HI0604 300 adenylate cyclase (cyaA) #15 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #16 HI0658 160 ABC transporter, ATP-binding protein #17 HI0967 25 H. influenzae predicted coding region HI0967 #18 HI0970 57 3-dehydroquinase (aroQ) #19 HI1587 300 DNA-binding protein H-NS (hns) #20 HI1588 69 formyltetrahydrofolate deformylase (purU) Motif number 1 CTCAACTCTCTACAACAGAAATAAAAACCCCACAGGC 3 41 0 TAACAAAAAA 0.567455 -30 GCTGACCGCGTGCAGAAAGGGTAAAAA 5 14 1 TAGAGAAAAA 0.873016 -17 AGATTAGCGTAAAAAAGACAGCAAAATGCCGCCTGAA 11 148 0 AAAAGAAAAT 0.961131 -52 TTTACCATTTAGATTAGGGAAAAATA 12 8 1 TAGAGAAAAA 0.873016 -19 AATTGAAAAATAGGCTAAAAATAGCGCGTA 13 4 1 TAAAGTAAAA 0.653264 -281 ATAAATTCCCTATAGAGGTTGAAAAATAGGGTGATTT 13 138 1 TAGAGAAAAT 0.916747 -147 TTCTAATGAAAATAAACTGCGTAAAAATGCAGAAGAT 13 213 0 AAAAGAAAAA 0.939167 -72 TCTAATTAAATTAAAAGTGAAATAAAATTCGATCATT 13 249 0 TAAAATAAAA 0.561721 -36 ACTTAGGGAGTATAAATGCAAAAAAATGTGACATAAA 14 230 0 TAAAAAAAAT 0.919065 -71 TCGGTAACCTATCAACCACAGGAAAATA 15 2 0 AAACGAAAAT 0.820649 -72 GCCACGTATAATAAGACGCAATAAAAACTATTTATAA 16 39 0 AAGAAAAAAA 0.873866 -122 CTTTTTTGACTAGAAAATCGATAAAATCGGAATAGAC 16 75 1 TAAAAAAAAT 0.919065 -86 CCGAGAAAAGAAAAAATATTGCAAAATAGCCTCAAAT 16 116 1 AAAAGAAAAT 0.961131 -45 TTCGACCACCAAAAATCGAAAAAACCAGTATAAT 18 8 1 AAAAGAAAAA 0.939168 -50 GGGAGATTACCGTAAAACAAACAAAATGCCAACAGAT 19 110 1 CAAAAAAAAT 0.726264 -191 TTATATTTTTATTAAAGTTTATAAAATTTTTATAAAA 19 146 0 AAAAAAAAAT 0.943888 -155 ATATAAAGAAAATAAACACAAAAAAATATATCTGTTT 19 177 1 AAAAAAAAAT 0.943888 -124 TTTATTTAATAATAGAGAAAATAAAATTTATTGTAAA 19 238 0 AAGAAAAAAT 0.917332 -63 AATAAATAACATTAAATGTGGGAAAATTTATTTAATA 19 264 0 AAAAGAAAAT 0.961129 -37 AATAAACCTCAATAAATAACATTAAAT 19 284 0 AAAAATAAAT 0.752531 -17 TAGATAAAAAAATAGAACCCATAAAATAGGTTCTAGT 20 25 0 AAGAAAAAAT 0.917332 -45 * *** * ***** Masking position 4 Map Score: 22.5361 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 319 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 2 TCATTCTTGAATATTTATTGGTATAGTAAGGG 1 32 1 ATATTTTGGT 0.54129 -151 AACTAGTACAATTTCGATTGTAAAGAAAAAAT 1 92 0 ATTTCTTGTA 0.686341 -91 TGCCGAAATTTTGCTTAATCCCCACAGCC 3 8 1 ATTTTTTAAT 0.599177 -63 TGGGGTTTTTATTTCTGTTGTAGAGAGTTGAG 3 46 1 ATTTCTTGTA 0.686341 -25 TTTGATCGCGATTTTCCTTAGTTAGCGCAGAA 4 59 0 ATTTTTTAGT 0.855892 -162 TAGAAAGATTATTTCTTCTATTCTAGACAAAT 9 37 1 ATTTCCTATT 0.850603 -93 TTAACGCGCTATTTTTGTTATTAGTCCTAGGT 13 42 1 ATTTTTTATT 0.94901 -243 ATGATTAAGAATTTTAACTATTCCATATTTAG 13 89 1 ATTTTCTATT 0.911458 -196 TACGCAGTTTATTTTCATTAGAAATGATCGAA 13 227 1 ATTTTTTAGA 0.641426 -58 ACCTTACTCAATATCACTTATTAAGGAAT 14 8 0 ATATCTTATT 0.743453 -293 ATAGCTTGATATTTTTCTTATCAACGCAAAGT 14 50 0 ATTTTTTATC 0.822923 -251 ATAAAAATCTATATTTTCTATTATTAGTGGAT 14 80 0 ATATTCTATT 0.743453 -221 TAAAAAAGTCATTTTGATTGTTGATAGGTAAA 14 170 1 ATTTTTTGTT 0.929256 -131 AATACTATAAATTTTACCTATCAACAATCAAA 14 182 0 ATTTTCTATC 0.719918 -119 TTGTTCGCCAATTTTTGTTGTTCTGGTAGGGA 14 273 1 ATTTTTTGTT 0.929256 -28 ATCTGTTGGCATTTTGTTTGTTTTACGGTAAT 19 115 0 ATTTTTTGTT 0.929256 -186 TTTTGTGTTTATTTTCTTTATATTTTTATTAA 19 168 0 ATTTTTTATA 0.848613 -133 TTTATTGTAAATATCTATTATTAAATAAATGG 19 217 0 ATATCTTATT 0.743453 -84 AATAAATTTTATTTTCTCTATTATTAAATAAA 19 243 1 ATTTTCTATT 0.911458 -58 CCCACATTTAATGTTATTTATTGAGGTTTATT 19 279 1 ATGTTTTATT 0.702406 -22 ***** ***** Masking position 4 Map Score: 17.3186 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 158 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 ATGTAATTTATTATTTACACT 1 2 1 TGTAATTTAT 0.831236 -181 CCAGCCTGTGGGGTTTTTATTTCTGTTGTA 3 38 1 GGGTTTTTAT 0.623518 -33 TCAATCAGAGGGGGATTTGTCTAGAATAGA 9 53 0 GGGGATTTGT 0.903762 -77 GTTCCATGATGATGATTTATCATTCAGGCG 11 126 1 GATGATTTAT 0.754794 -74 AATCTTACCCGGTGATTTATCGCCAGAGCG 11 180 1 GGTGATTTAT 0.975042 -20 AACCTCTATAGGGAATTTATTTTCCACGAG 13 128 0 GGGAATTTAT 0.925672 -157 TGAAAAATAGGGTGATTTATTGCGATAATC 13 157 1 GGTGATTTAT 0.975042 -128 TATTGAGTAAGGTATTTTATAATACTTTGC 14 27 1 GGTATTTTAT 0.831471 -274 TTCGAAAAATTGTGATTTATGTCACATTTT 14 215 1 TGTGATTTAT 0.906341 -86 CTCCCTAAGTGGTAAATTGTTCGCCAATTT 14 257 1 GGTAAATTGT 0.492301 -44 CCACATTTAATGTTATTTATTGAGGTTTAT 19 280 1 TGTTATTTAT 0.725264 -21 ********** Masking position 7 Map Score: 7.23315 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 322 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 GGCTTGCATCACACAAAAGAATCTCTCGGAT 2 39 0 ACACAAAGAA 0.928795 -160 AAACCGATAGCCACAGGAATAATGTATTACC 2 123 1 CCACAGAATA 0.857521 -76 ACTCAACTCTCTACAACAGAAATAAAAACCC 3 48 0 CTACAAAGAA 0.789156 -23 AAACACGCAAACACAACAATAACGGAGCCGT 6 13 1 ACACAAAATA 0.89242 -22 AGCGTAAAAAAGACAGCAAAATGCCGCCTGA 11 149 0 AGACAGAAAA 0.67983 -51 TAAGCTATTTACGCAATAAAACTAGGTACTA 14 123 1 ACGCAAAAAA 0.928795 -178 GGGAGTATAAATGCAAAAAAATGTGACATAA 14 231 0 ATGCAAAAAA 0.763652 -70 AACCTATCAACCACAGGAAAATA 15 3 0 CCACAGAAAA 0.944222 -71 GTATAATAAGACGCAATAAAAACTATTTATA 16 40 0 ACGCAAAAAA 0.928795 -121 GTATAATGTGCCACACAAAAAGGATTAAAA 18 38 1 CCACACAAAA 0.863294 -20 TCCCCAATCACTACAAAAGTAGAGGCGCAAT 19 83 0 CTACAAAGTA 0.570944 -218 AAGAAAATAAACACAAAAAAATATATCTGTT 19 182 1 ACACAAAAAA 0.958902 -119 ****** **** Masking position 5 Map Score: 6.07951 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 248 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 TTTGATGGTATGATCGCTATTCTCATGACA 1 122 1 TGATCGCTAT 0.955386 -61 TTTCCCCAATAGGTCGCAATGCGGCGAAAG 1 156 0 AGGTCGCAAT 0.969048 -27 TCAGTGACACACATCGCAATGAGTAAAACC 2 87 0 ACATCGCAAT 0.914713 -112 GTATTACCTGTGGTCGCAATCGATTGACCG 2 146 1 TGGTCGCAAT 0.983171 -53 AGTTTGTTTTTGATCGCGATTTTCCTTAGT 4 69 0 TGATCGCGAT 0.96946 -152 ATGGGGTAGATTATCGCAATAAATCACCCT 13 165 0 TTATCGCAAT 0.931039 -120 ********** Masking position 4 Map Score: 2.70414 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 92 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 CTATCGGTTTTATCATTCAGTGACACACAT 2 103 0 TATCATTCAG 0.922118 -96 GTAACGAAATTATCTTTCAGCAAGGAGCT 4 202 1 TATCTTTCAG 0.970008 -19 GATGATGATTTATCATTCAGGCGGCATTTT 11 133 1 TATCATTCAG 0.922118 -67 ATTTTTAGCCTATTTTTCAATT 13 3 0 TATTTTTCAA 0.927824 -282 TAAATCACCCTATTTTTCAACCTCTATAGG 13 146 0 TATTTTTCAA 0.927824 -139 AAATTTATAGTATTTTTCGAAAAATTGTGA 14 200 1 TATTTTTCGA 0.879219 -101 TAAGTATAGATATCTTTCGGTAACCTATCA 15 25 0 TATCTTTCGG 0.948225 -49 AATTTGAGGCTATTTTGCAATATTTTTTCT 16 124 0 TATTTTGCAA 0.773468 -37 ********** Masking position 2 Map Score: 5.66528 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 114 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 TTTTCACTTTAAGTGGAATTTTTTCTTTACAAT 1 75 1 AGTGGATTTT 0.965367 -108 TGTGTGATGCAAGCCACATTTTTGCCCTCAACG 2 55 1 AGCCAATTTT 0.855106 -144 TAATAAAACAAGGTGCGATTCTT 8 41 1 AGTGCATTTT 0.965367 -13 ACAGCCGTAAAAGCGGTAATGTTTTTACGCTGA 11 11 1 AGCGGAATTT 0.90187 -189 TTTATCATTCAGGCGGCATTTTGCTGTCTTTTT 11 141 1 AGCGGATTTG 0.931607 -59 CGCGTTAAATACGCGCTATTTTTAGCCTATTTT 13 17 0 AGCGCATTTT 0.984921 -268 CGCGTATTTAACGCGCTATTTTTGTTATTAGTC 13 35 1 AGCGCATTTT 0.984921 -250 ATTGTGATTTATGTCACATTTTTTTGCATTTAT 14 223 1 AGTCAATTTT 0.715791 -78 GTCTTATTATACGTGGCTTTTTTGACTAGAAAA 16 59 1 AGTGGTTTTT 0.796835 -102 ACAAAAGTAGAGGCGCAATTATTATAAGTATTT 19 69 0 AGCGCATTTT 0.984921 -232 * **** *** ** Masking position 10 Map Score: 8.77796 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 115 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 CGTGGGTTTTCCCCAATAGGTCGCAAT 1 166 0 TTTCCCCAAT 0.777422 -17 TGCCGAAATTTTGCTTAATCCCCACAGCC 3 10 1 TTTGCTTAAT 0.696813 -61 TGATCGCGATTTTCCTTAGTTAGCGCAGAA 4 59 0 TTTCCTTAGT 0.776486 -162 TCTCCGACGGTTTACATAATTACTATACTG 4 160 0 TTTACATAAT 0.680328 -61 TCATTTCTTTAATTCAGCATAAG 7 4 1 TTTCTTTAAT 0.878861 -59 TATTTTTCCCTAATCTAAATGGTA 12 13 0 TTTCCCTAAT 0.956793 -14 TGTTCTTTATCTAATTAAATTAAAA 13 270 0 TTTATCTAAT 0.932436 -15 AAATGACTTTTTTACCTAAGAGTGGTAGGA 14 154 0 TTTACCTAAG 0.766421 -147 ATCTACAATTTATCTAGTAAAAGAGGAA 15 56 0 TTTATCTAGT 0.827448 -18 GTTTCGACCATTTATTTAATAATAGATATT 19 210 1 TTTATTTAAT 0.862167 -91 TAAATTTTATTTTCTCTATTATTAAATAAA 19 245 1 TTTCTCTATT 0.670686 -56 TGTGGGAAAATTTATTTAATAATAGAGAAA 19 255 0 TTTATTTAAT 0.862167 -46 GTTCTATTTTTTTATCTAAACATAGCACAC 20 44 1 TTTATCTAAA 0.611198 -26 ********** Masking position 8 Map Score: 4.84076 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 102 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 9 CACTGAATGATAAAACCGATAGCCACAGGA 2 111 1 TAAAACCGAT 0.709233 -88 ACAGCCGTAAAAGCGGTAATGTTTTTA 11 8 1 TAAAAGCGGT 0.931957 -192 CCTGCGCGCGTCAAATAGATGAAACACGTT 11 43 0 TCAAATAGAT 0.768949 -157 GCACCAACTCTCAAATCGGTACTCCTTGTA 11 82 0 TCAAATCGGT 0.952268 -118 ATTTATCTAGTAAAAGAGGAAATAAGTATA 15 47 0 TAAAAGAGGA 0.785264 -27 AGAAAATCGATAAAATCGGAATAGACTGTT 16 86 1 TAAAATCGGA 0.926941 -75 AAAATTTTTATAAAATCTGTTGGCATTTTG 19 131 0 TAAAATCTGT 0.703368 -170 GGTTCTAGTTTCAAATAGAAAAA 20 4 0 TCAAATAGAA 0.635802 -66 ATAGAACCCATAAAATAGGTTCTAGTTTCA 20 21 0 TAAAATAGGT 0.924874 -49 ********** Masking position 5 Map Score: 1.75329 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 295 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 GGTCGCAATGCGGCGAAAGCCGGTGTCATG 1 145 0 CGGCGAAAGC 0.899612 -38 TGCCGAAATTTTGCTTAATC 3 1 1 TGCCGAAATT 0.885199 -70 CCTTAGTTAGCGCAGAAAGAGTTATTTATC 4 46 0 CGCAGAAAGA 0.84785 -175 AGCTCCTTGCTGAAAGATAATTTCGTT 4 204 0 TGCTGAAAGA 0.866043 -17 GCTGACCGCGTGCAGAAAGGGTAAAAA 5 14 1 TGCAGAAAGG 0.837017 -17 TAAGTTGTTATGGCGAAATCAGCACTGTTC 7 30 1 TGGCGAAATC 0.903206 -33 AGCTTAATTCTGCCGATATAAAAATCTATA 14 99 0 TGCCGATATA 0.799968 -202 GTTGATAGGTTACCGAAAGATATCTATACT 15 23 1 TACCGAAAGA 0.830114 -51 AAGGAATAGTTGCCGAAATCAAATAAA 19 8 0 TGCCGAAATC 0.96839 -293 ********** Masking position 6 Map Score: 1.70429 Number of sites scoring better than the average of aligned sites = 1219 Number in coding regions = 1166 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 11 TACATTATTCCTGTGGCTATCGGTTTTATC 2 119 0 CTGTGGCTAT 0.947566 -80 CACAGGCTGGCTGTGGGGATTAAGCAAAAT 3 18 0 CTGTGGGGAT 0.989508 -53 CACAGCCAGCCTGTGGGGTTTTTATTTCTG 3 33 1 CTGTGGGGTT 0.966289 -38 CTGAACACATCTCTGGAGATTT 9 3 0 CTCTGGAGAT 0.959509 -127 CGCTCTGGCGATAAATCACCGG 11 188 0 CTCTGGCGAT 0.984786 -12 ********** Masking position 4 Map Score: 2.60869 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 67 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 AAAAACATCGGCTTTTTGCTAATAATCCGA 2 15 1 GCTTTTTGCT 0.956161 -184 AGCTCCTTGCTGAAAGATAAT 4 210 0 GCTCCTTGCT 0.981656 -11 AACCAGTGAGGCCCTTCGCTTCCCGGATTC 8 12 0 GCCCTTCGCT 0.969126 -42 AAGAATCGCACCTTGTTTTATTAACCA 8 37 0 GCACCTTGTT 0.852452 -17 GAGAGTTGGTGCTCTTCGCTGCCTGCGTTC 11 100 1 GCTCTTCGCT 0.981656 -100 CATTCAGGCGGCATTTTGCTGTCTTTTTTA 11 146 1 GCATTTTGCT 0.938353 -54 ********** Masking position 6 Map Score: 2.51474 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 151 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 ********** No masking Map Score: 2.41828e-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: 2.41828e-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: 2.41828e-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