AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i038_Galactose_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 galE 260 UDP-galactose-4-epimerase #2 modF 67 ATP-binding component of molybdate transport system #3 modE 128 molybdate uptake regulatory protein #4 HI0351 172 UDP-glucose 4-epimerase (galE) #5 HI0352 300 conserved hypothetical protein #6 HI0819 37 galactokinase (galK) #7 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) Motif number 1 AGAGGGTTTATGAATGATTGCGCTTTTTAT 1 103 0 TGAATGATTG 0.987587 -158 ATTGATTGATTGATTGATTGATT 5 4 0 TGATTGATTG 0.998405 -297 ATTGATTGATTGATTGATTGATTGATTGAT 5 16 0 TGATTGATTG 0.998405 -285 ATTGATTGATTGATTGATTGATTGATTGAT 5 36 0 TGATTGATTG 0.998405 -265 ATTGATTGATTGATTGATTGATTGATTGAT 5 48 0 TGATTGATTG 0.998405 -253 ATTGATTGATTGATTGATTGATTGATTGAT 5 60 0 TGATTGATTG 0.998405 -241 ATTGATTGATTGATTGATTGATTGATTGAT 5 72 0 TGATTGATTG 0.998405 -229 ATTGATTGATTGATTGATTGATTGATTGAT 5 84 0 TGATTGATTG 0.998405 -217 ATTGATTGATTGATTGATTGATTGATTGAT 5 96 0 TGATTGATTG 0.998405 -205 TGACAGACTTTGATTGATTGATTGATTGAT 5 108 0 TGATTGATTG 0.998405 -193 CTTCAAAATAAAATTGATTGCAACGGAAAA 5 204 0 AAATTGATTG 0.862417 -97 ********** Masking position 7 Map Score: 51.4521 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 AGAGGGTTTATGAATGATTGCGCTTTTTAT 1 103 0 TGAATGATTG 0.988311 -158 ATTGATTGATTGATTGATTGATT 5 4 0 TGATTGATTG 0.998499 -297 ATTGATTGATTGATTGATTGATTGATTGAT 5 16 0 TGATTGATTG 0.998499 -285 ATTGATTGATTGATTGATTGATTGATTGAT 5 36 0 TGATTGATTG 0.998499 -265 ATTGATTGATTGATTGATTGATTGATTGAT 5 48 0 TGATTGATTG 0.998499 -253 ATTGATTGATTGATTGATTGATTGATTGAT 5 60 0 TGATTGATTG 0.998499 -241 ATTGATTGATTGATTGATTGATTGATTGAT 5 72 0 TGATTGATTG 0.998499 -229 ATTGATTGATTGATTGATTGATTGATTGAT 5 84 0 TGATTGATTG 0.998499 -217 ATTGATTGATTGATTGATTGATTGATTGAT 5 96 0 TGATTGATTG 0.998499 -205 TGACAGACTTTGATTGATTGATTGATTGAT 5 108 0 TGATTGATTG 0.998499 -193 CTTCAAAATAAAATTGATTGCAACGGAAAA 5 204 0 AAATTGATTG 0.869473 -97 ********** Masking position 7 Map Score: 51.4521 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 AGAGGGTTTATGAATGATTGCGCTTTTTAT 1 103 0 TGAATGATTG 0.986685 -158 ATTGATTGATTGATTGATTGATT 5 4 0 TGATTGATTG 0.998288 -297 ATTGATTGATTGATTGATTGATTGATTGAT 5 16 0 TGATTGATTG 0.998288 -285 ATTGATTGATTGATTGATTGATTGATTGAT 5 36 0 TGATTGATTG 0.998288 -265 ATTGATTGATTGATTGATTGATTGATTGAT 5 48 0 TGATTGATTG 0.998288 -253 ATTGATTGATTGATTGATTGATTGATTGAT 5 60 0 TGATTGATTG 0.998288 -241 ATTGATTGATTGATTGATTGATTGATTGAT 5 72 0 TGATTGATTG 0.998288 -229 ATTGATTGATTGATTGATTGATTGATTGAT 5 84 0 TGATTGATTG 0.998288 -217 ATTGATTGATTGATTGATTGATTGATTGAT 5 96 0 TGATTGATTG 0.998288 -205 TGACAGACTTTGATTGATTGATTGATTGAT 5 108 0 TGATTGATTG 0.998288 -193 CTTCAAAATAAAATTGATTGCAACGGAAAA 5 204 0 AAATTGATTG 0.853765 -97 ********** Masking position 7 Map Score: 51.4521 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 AGAGGGTTTATGAATGATTGCGCTTTTTAT 1 103 0 TGAATGATTG 0.985745 -158 ATTGATTGATTGATTGATTGATT 5 4 0 TGATTGATTG 0.998166 -297 ATTGATTGATTGATTGATTGATTGATTGAT 5 16 0 TGATTGATTG 0.998166 -285 ATTGATTGATTGATTGATTGATTGATTGAT 5 36 0 TGATTGATTG 0.998166 -265 ATTGATTGATTGATTGATTGATTGATTGAT 5 48 0 TGATTGATTG 0.998166 -253 ATTGATTGATTGATTGATTGATTGATTGAT 5 60 0 TGATTGATTG 0.998166 -241 ATTGATTGATTGATTGATTGATTGATTGAT 5 72 0 TGATTGATTG 0.998166 -229 ATTGATTGATTGATTGATTGATTGATTGAT 5 84 0 TGATTGATTG 0.998166 -217 ATTGATTGATTGATTGATTGATTGATTGAT 5 96 0 TGATTGATTG 0.998166 -205 TGACAGACTTTGATTGATTGATTGATTGAT 5 108 0 TGATTGATTG 0.998166 -193 CTTCAAAATAAAATTGATTGCAACGGAAAA 5 204 0 AAATTGATTG 0.844917 -97 ********** Masking position 7 Map Score: 51.4521 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 AGAGGGTTTATGAATGATTGCGCTTTTTAT 1 103 0 TGAATGATTG 0.986231 -158 ATTGATTGATTGATTGATTGATT 5 4 0 TGATTGATTG 0.998229 -297 ATTGATTGATTGATTGATTGATTGATTGAT 5 16 0 TGATTGATTG 0.998229 -285 ATTGATTGATTGATTGATTGATTGATTGAT 5 36 0 TGATTGATTG 0.998229 -265 ATTGATTGATTGATTGATTGATTGATTGAT 5 48 0 TGATTGATTG 0.998229 -253 ATTGATTGATTGATTGATTGATTGATTGAT 5 60 0 TGATTGATTG 0.998229 -241 ATTGATTGATTGATTGATTGATTGATTGAT 5 72 0 TGATTGATTG 0.998229 -229 ATTGATTGATTGATTGATTGATTGATTGAT 5 84 0 TGATTGATTG 0.998229 -217 ATTGATTGATTGATTGATTGATTGATTGAT 5 96 0 TGATTGATTG 0.998229 -205 TGACAGACTTTGATTGATTGATTGATTGAT 5 108 0 TGATTGATTG 0.998229 -193 CTTCAAAATAAAATTGATTGCAACGGAAAA 5 204 0 AAATTGATTG 0.849471 -97 ********** Masking position 7 Map Score: 51.4521 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 AGAGGGTTTATGAATGATTGCGCTTTTTAT 1 103 0 TGAATGATTG 0.985745 -158 ATTGATTGATTGATTGATTGATT 5 4 0 TGATTGATTG 0.998166 -297 ATTGATTGATTGATTGATTGATTGATTGAT 5 16 0 TGATTGATTG 0.998166 -285 ATTGATTGATTGATTGATTGATTGATTGAT 5 36 0 TGATTGATTG 0.998166 -265 ATTGATTGATTGATTGATTGATTGATTGAT 5 48 0 TGATTGATTG 0.998166 -253 ATTGATTGATTGATTGATTGATTGATTGAT 5 60 0 TGATTGATTG 0.998166 -241 ATTGATTGATTGATTGATTGATTGATTGAT 5 72 0 TGATTGATTG 0.998166 -229 ATTGATTGATTGATTGATTGATTGATTGAT 5 84 0 TGATTGATTG 0.998166 -217 ATTGATTGATTGATTGATTGATTGATTGAT 5 96 0 TGATTGATTG 0.998166 -205 TGACAGACTTTGATTGATTGATTGATTGAT 5 108 0 TGATTGATTG 0.998166 -193 CTTCAAAATAAAATTGATTGCAACGGAAAA 5 204 0 AAATTGATTG 0.844917 -97 ********** Masking position 7 Map Score: 51.4521 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ATAAAAAGCGCAATCATTCATAAACCCTCT 1 103 1 CAATCATTCA 0.986231 -158 AATCAATCAATCAATCAATCAAT 5 4 1 CAATCAATCA 0.998229 -297 ATCAATCAATCAATCAATCAATCAATCAAT 5 16 1 CAATCAATCA 0.998229 -285 ATCAATCAATCAATCAATCAATCAATCAAT 5 36 1 CAATCAATCA 0.998229 -265 ATCAATCAATCAATCAATCAATCAATCAAT 5 48 1 CAATCAATCA 0.998229 -253 ATCAATCAATCAATCAATCAATCAATCAAT 5 60 1 CAATCAATCA 0.998229 -241 ATCAATCAATCAATCAATCAATCAATCAAT 5 72 1 CAATCAATCA 0.998229 -229 ATCAATCAATCAATCAATCAATCAATCAAT 5 84 1 CAATCAATCA 0.998229 -217 ATCAATCAATCAATCAATCAATCAATCAAT 5 96 1 CAATCAATCA 0.998229 -205 ATCAATCAATCAATCAATCAAAGTCTGTCA 5 108 1 CAATCAATCA 0.998229 -193 TTTTCCGTTGCAATCAATTTTATTTTGAAG 5 204 1 CAATCAATTT 0.849471 -97 ********** Masking position 6 Map Score: 51.4521 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 ATCGTTTACACAAGAATTTAGCCGTTTTTT 1 158 0 CAAGAATTTA 0.972537 -103 TAAACGATTCCACTAATTTATTCCATGTCA 1 180 1 CACTAATTTA 0.899771 -81 AGAATAGTCTCATGACTATATCTGGAGTTG 3 14 0 CATGACTATA 0.781093 -115 CTCGCTACAACAATACTTTTTAGCAACAGG 4 67 1 CAATACTTTT 0.735963 -106 TGGTGATTTTCAATAAAATAAAAAACCTGT 4 92 0 CAATAAAATA 0.91747 -81 TTTTTAGTCTCAATAATTAACAAGGAAATC 4 150 1 CAATAATTAA 0.83294 -23 ATTTTCTTGCCAAGAAAATAATGATCTTCA 5 229 0 CAAGAAAATA 0.901435 -72 ATTTTCTTGGCAAGAAAATAAAAAAAGTAT 5 240 1 CAAGAAAATA 0.901435 -61 AATTTTTGAGCAATACTATACTTTT 5 286 1 CAATACTATA 0.94589 -15 TTTTGATCATAAATAATTTACGATAAATTG 7 45 1 AAATAATTTA 0.755419 -163 GGTTTATTTACAATAATTTAGTATAAATTA 7 151 1 CAATAATTTA 0.977296 -57 TAAACGATTACATTAATTTATACTAAATTA 7 164 0 CATTAATTTA 0.914388 -44 ********** Masking position 5 Map Score: 11.3925 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 124 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 AATTTAGCCGTTTTTTATGCGCGATTAAGT 1 144 0 TTTTTTATGC 0.96227 -117 TTTTCGCATCTTTGTTATGCTATGGTTATT 1 213 1 TTTGTTATGC 0.916433 -48 GTGTTGACAATTTGTTATGAAACACGTATC 2 13 1 TTTGTTATGA 0.900805 -55 TAGCAACAGGTTTTTTATTTTATTGAAAAT 4 87 1 TTTTTTATTT 0.929794 -86 AGTGATATAATTTTTTAGTCTCAATAATTA 4 139 1 TTTTTTAGTC 0.769337 -34 AAAAAATACTTTTTTTATTTTCTTGCCAAG 5 245 0 TTTTTTATTT 0.929794 -56 AAAAAAAGTATTTTTTAATTGTTCTACAAT 5 259 1 TTTTTTAATT 0.650779 -42 TTATCGTAAATTATTTATGATCAAAATATA 7 41 0 TTATTTATGA 0.728519 -167 ATAAGCAAAATTTTTTATGATTTAGTTCAT 7 96 0 TTTTTTATGA 0.954792 -112 TTTTGCTTATTTTCTTATTTTGTGACAAAG 7 116 1 TTTCTTATTT 0.755759 -92 TTGACTCCTGTTTTTTATCAATGTAAACGA 7 187 0 TTTTTTATCA 0.828841 -21 ********** Masking position 7 Map Score: 9.16126 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 171 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 10 CTCTCCGGCCAACGGTTCGACGCATGCAGG 1 50 1 AACGGTTCGA 0.944571 -211 TGAAAAAAGACGCGGTTTCATGCCTGCATG 1 72 0 CGCGGTTTCA 0.903932 -189 TTCTTGTGTAAACGATTCCACTAATTTATT 1 172 1 AACGATTCCA 0.951346 -89 CACTTTGTGCAGCGATTACTGACAGGGATA 2 39 0 AGCGATTACT 0.954894 -29 TTCTGTGCTTAGCGGTTAGAATAGTCTCAT 3 31 0 AGCGGTTAGA 0.976987 -98 ATAAATTGAAAGCGGTTACTTTCATAAGTA 7 67 1 AGCGGTTACT 0.977661 -141 TATCAATGTAAACGATTACATTAATTTATA 7 172 0 AACGATTACA 0.959326 -36 ********** Masking position 6 Map Score: 5.32584 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 333 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 GGAGGCGGCCTTAGCACCCTCTCCGGCCAAC 1 32 1 TTAGACCCTC 0.846112 -229 TATGCTATGGTTATTTCATACCATAAGCCTA 1 228 1 TTATTCATAC 0.928396 -33 TGACAATTTGTTATGAAACACGTATCCCTGT 2 17 1 TTATAAACAC 0.750234 -51 TTTATATCCCACTTTGTGCAGC 2 56 0 TTATTCCCAC 0.973215 -12 ATAACCTTATATCACACAACTAATGGA 4 7 1 TTATTCACAC 0.980748 -166 ATATGAGAGGTTATCTCACTCGCTACAACAA 4 49 1 TTATTCACTC 0.958555 -124 ATCACCATTCTTACCACACAAAATAGTGATA 4 115 1 TTACACACAA 0.723277 -58 GACTAAAAAATTATATCACTATTTTGTGTGG 4 128 0 TTATTCACTA 0.867084 -45 TGACTATAGTTTATTACCTAAAGATTATGAT 5 172 1 TTATACCTAA 0.583801 -129 TTTTTATGATTTAGTTCATACTTATGAAAGT 7 84 0 TTAGTCATAC 0.871199 -124 **** ****** Masking position 3 Map Score: 5.94178 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 239 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 12 GCGAAAAGTGTGACATGGAATAAATTAGTG 1 190 0 TGACATGGAA 0.960716 -71 AACCATAGCATAACAAAGATGCGAAAAGTG 1 210 0 TAACAAAGAT 0.945469 -51 CAGCGATTACTGACAGGGATACGTGTTTCA 2 30 0 TGACAGGGAT 0.973223 -38 TCTCAATAATTAACAAGGAAATCATT 4 157 1 TAACAAGGAA 0.980878 -16 TTATAGATTATAACAAGGAAAAAGTT 7 7 0 TAACAAGGAA 0.980878 -201 TCTTATTTTGTGACAAAGATCACGGTTTAT 7 128 1 TGACAAAGAT 0.964618 -80 ********** Masking position 5 Map Score: 6.18035 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 38 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 TTATATCCCACTTTGTGCAGCGATTACTGA 2 47 0 CTTTGTGCAG 0.969674 -21 AGCACTCCCCTTTTGTGCGGTCAGCTTTGC 3 62 1 TTTTGTGCGG 0.987977 -67 GTGCGGTCAGCTTTGCGTGGCGTTCGTTTT 3 76 1 CTTTGCGTGG 0.979649 -53 TATATCACTATTTTGTGTGGTAAGAATGGT 4 118 0 TTTTGTGTGG 0.981525 -55 ********** Masking position 4 Map Score: 1.70686 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 49 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 AACCCTCTGTTTTATAATCACTTAATCGCG 1 125 1 TTTATAATCA 0.954632 -136 TTTTATTTTATTGAAAATCACCATTCTTAC 4 99 1 TTGAAAATCA 0.970193 -74 ATGGAACAAGTTTAAAATCAATTGACTATA 5 150 1 TTTAAAATCA 0.967899 -151 CAATTTTATTTTGAAGATCATTATTTTCTT 5 218 1 TTGAAGATCA 0.972327 -83 TCGTAAATTATTTATGATCAAAATATAAGA 7 38 0 TTTATGATCA 0.957833 -170 ********** Masking position 4 Map Score: 4.10316 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 80 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 15 GCTTTTTATCTGAAAAAAGACGCGGTTTCA 1 82 0 TGAAAAAAGA 0.840379 -179 AAGTGTGACATGGAATAAATTAGTGGAATC 1 185 0 TGGAATAAAT 0.675131 -76 CAATTTGTTATGAAACACGTATCCCTGTCA 2 20 1 TGAAACACGT 0.886129 -48 CTTATTGTGACGGAAAACGAACGCCACGCA 3 89 0 CGGAAAACGA 0.882398 -40 AACAATGTCCTGGCAAAAGTCTTATTGTGA 3 109 0 TGGCAAAAGT 0.922344 -20 TTGCAGGTAATGGAACAAGTTTAAAATCAA 5 141 1 TGGAACAAGT 0.966427 -160 TTGATTGCAACGGAAAACATCATAATCTTT 5 191 0 CGGAAAACAT 0.823805 -110 GGCAAGAAAATAAAAAAAGTATTTTTTAAT 5 248 1 TAAAAAAAGT 0.620251 -53 GATTATAACAAGGAAAAAGTT 7 2 0 AGGAAAAAGT 0.913448 -206 ********** Masking position 5 Map Score: 1.05046 Number of sites scoring better than the average of aligned sites = 1370 Number in coding regions = 1261 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528