AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inagC_ecoli_hinf_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 nagD 47 N-acetylglucosamine metabolism #2 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #3 nagB_nagE 332 nagB: glucosamine-6-phosphate deaminase, nagE: PTS system, N-acetylglucosamine-specific enzyme IIABC #4 manX 300 PTS enzyme IIAB, mannose-specific #5 manY 62 PTS enzyme IIC, mannose-specific #6 glmS 161 L-glutamine:D-fructose-6-phosphate aminotransferase #7 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #8 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #9 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #10 HI0429 111 glucosamine--fructose-6-phosphate aminotransferase (glmS) #11 HI0642 159 UDP-N-acetylglucosamine pyrophosphorylase (glmU) Motif number 1 TCACAAAAGACACGCGTTTAATTTGCGATAC 3 142 0 CCGCGTTTAA 0.942388 -191 GTTATTATCACTCCCTTTTACTGGCTAAACC 3 191 1 CCCCTTTTAC 0.973593 -142 ATATGTTTAACTCCCGTTTAACAACCATGGA 4 17 0 CCCCGTTTAA 0.973593 -284 TGTACTTCTCCTGTTTACGTAAGACTTA 5 45 0 CCCTGTTTAC 0.991777 -18 AACCTGTATGCCCGTTTTTTCGGGCGCCCCG 6 108 0 CCGTTTTTTC 0.911603 -54 ATATAAAACCCCCCTGTTTTCCTGTTTATTC 7 55 1 CCCTGTTTTC 0.988007 -246 ACCATCGTCACGCCTTTTGTCTGCAGAAAAT 7 144 0 CCCTTTTGTC 0.828985 -157 AACTTACCTCCCCCTGTTTTATTCCGTTACA 9 28 1 CCCTGTTTTA 0.958752 -258 CACTTTCCTTCCCCTGTTTACGGGGGAAGGT 9 81 1 CCCTGTTTAC 0.991777 -205 TTACATTTGCCACGCGTTTACACAATAAAAA 10 55 0 CCGCGTTTAC 0.983043 -57 * ********* Masking position 7 Map Score: 15.9624 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 241 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 TTGTTATCCCTGCCCTGGCTCCTTGCT 2 8 1 CCCTGCCCTG 0.925288 -52 CTTATTCCCCCTACGAGAACCCT 3 4 1 ATTCCCCCTA 0.940525 -329 ACAGGCGTCAATCCGACCTGATTTTTTGAA 3 240 0 ATCCGACCTG 0.84938 -93 TGTACTTCTCCTGTTTACGTAAG 5 50 0 ACTTCTCCTG 0.785561 -13 ATAACATAATCTCCCTCCCACAAGCAGTAA 6 47 1 CTCCCTCCCA 0.54533 -115 GCGCGTGTGACCCGTCCTGAATAGCGTTC 7 10 1 ACCCGTCCTG 0.929863 -291 GCTGATATAAAACCCCCCTGTTTTCCTGTT 7 51 1 AACCCCCCTG 0.923354 -250 AGAGCAAAAACATCCACCTGACGCTTAAAT 7 99 1 CATCCACCTG 0.562467 -202 ATAACGGATTATCCCCGCTGACGAAAGCGC 7 183 0 ATCCCCGCTG 0.770703 -118 ACGCGTCCTGACTGTAATTT 7 291 0 ACGCGTCCTG 0.718211 -10 GGCGAATGTAATTCGCCCCTACATAAAGAT 8 24 0 ATTCGCCCCT 0.766712 -249 GGCGAATTACATTCGCCCTATAATCTCAAC 8 37 1 ATTCGCCCTA 0.940525 -236 GGCGAATGTAATTCGCCCCTACATAAAGAT 8 160 0 ATTCGCCCCT 0.766712 -113 GGCGAATTACATTCGCCCTATAATCACAAA 8 173 1 ATTCGCCCTA 0.940525 -100 CGTAAGGACAATTTGCCCTATGATTGTTTG 8 199 0 ATTTGCCCTA 0.795999 -74 AAAAAACTTACCTCCCCCTGTTTTATTCCG 9 24 1 CCTCCCCCTG 0.98252 -262 CAAGCACTTTCCTTCCCCTGTTTACGGGGG 9 77 1 CCTTCCCCTG 0.932747 -209 CCTTCGGGCACCTTCCCCCGTAAACAGGGG 9 91 0 CCTTCCCCCG 0.868865 -195 ********** Masking position 8 Map Score: 14.7362 Number of sites scoring better than the average of aligned sites = 2490 Number in coding regions = 2238 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 3 ATAATAACGATATTTGGTGACAAAACTCACAAAAG 3 164 0 TATGACAAAA 0.808869 -169 AAAACTTATTTTATCATTCAAAAAATCAGGTCGGA 3 224 1 TTTCAAAAAA 0.883297 -109 CGATTTATTTTAGATATCGAAAAAATTATTTTATG 4 162 0 TAAGAAAAAA 0.913324 -139 CTGCCTTAATTTTCTGCAGACAAAAGGCGTGACGA 7 136 1 TTCGACAAAA 0.767877 -165 CTCTGTCCATTTCACGATGAAAAAAATGTAGTTTT 7 226 1 TTAGAAAAAA 0.967358 -75 TTTAAACCGCTTCACCTTGAAAAAACTACATTTTT 7 247 0 TTAGAAAAAA 0.967358 -54 ATATTTAAATTAGAAAAAACTTACCTCCC 9 5 1 TTAGAAAAAA 0.967191 -281 GCTGTTCTGTTTGTAACGGAATAAAACAGGGGGAG 9 35 0 TTTGAATAAA 0.925525 -251 AAAACAAACTTAGTAATAGAATAAATAAGGAAAAC 10 85 1 TATGAATAAA 0.816582 -27 TTTAACCACTTTAAAATTCAAAAAACCGATGGGAA 11 18 1 TTACAAAAAA 0.86431 -142 TAACAAACTTTTATATAAGAAAAAACCGATGGTTT 11 51 0 TTTGAAAAAA 0.971909 -109 TTACCCGTTGTTATTGATGAATAAAGAGAAAATTT 11 135 1 TTTGAATAAA 0.925723 -25 ** * ******* Masking position 10 Map Score: 9.19573 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 189 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 ATTTGCGATACGAATTAAATTTTCACACACTCT 3 120 0 CGATTAATTT 0.973756 -213 AATCCGCCAACGGCTTACATTTTACTTATTGAG 3 303 1 CGGTTAATTT 0.974468 -30 CTGCGTTTCGCGATTTATTTTAGATATCGAAAA 4 174 0 CGATTATTTG 0.917126 -127 TTTTTGATTCCGATTTATATCGTTGTCGGTCAA 6 137 0 CGATTAATCT 0.911827 -25 CAAGGTGAAGCGGTTTAAATTCGTTCTCAAATT 7 263 1 CGGTTAATTG 0.96228 -38 TATGTAGGGGCGAATTACATTCGCCCTATAATC 8 29 1 CGATTAATTG 0.90374 -244 TATGTAGGGGCGAATTACATTCGCCCTATAATC 8 165 1 CGATTAATTG 0.90374 -108 TCAATAACAACGGGTAATATTCTATCTTAGAAA 11 119 0 CGGTAAATTT 0.872362 -41 *** *** *** * Masking position 7 Map Score: 7.73907 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 TTGCAAACGAATGTGACAAGGATATTTTACCTTT 4 85 1 ATTAAGGATA 0.951034 -216 AAATTATTTTATGTGATGAAGATCCGTAATTTAA 4 141 0 ATTAAAGATC 0.929665 -160 CTTAAGTCTTACGTAAACAGGAGAAGTACA 5 43 1 ACTAAGGAGA 0.814412 -20 ACCCGGTCACATGGGATGAGGAGATAACATAATC 6 24 1 ATGAAGGAGA 0.93743 -138 GGGGGGTTTTATATCAGCAGGATCTATGTGAACG 7 35 0 ATTAAGGATC 0.968723 -266 TTATTCATTGATCGAAATAAGAGCAAAAACATCC 7 80 1 ATGAAAGAGC 0.910683 -221 TCATCGTGAAATGGACAGAGGATAAATTGTTCAA 7 212 0 ATGCAGGATA 0.742528 -89 TCGCCCTATAATCTCAACAAGAGCTAAAAGTGAA 8 49 1 ATTAAAGAGC 0.934727 -224 CCAGCCTACGATATGAATAGGATCATCACGGTCA 9 243 1 ATTAAGGATC 0.968723 -43 GTAATATTCTATCTTAGAAAGATAGCAAATGGTA 11 105 0 ATTAAAGATA 0.89234 -55 ** * * ****** Masking position 9 Map Score: 6.07646 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 34 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 GCTCGTTTCAAGCCGTATTTTTATTTTGCT 3 39 1 AGCCGTATTT 0.889764 -294 TGTGATGAAGATCCGTAATTTAACTTTCGA 4 134 0 ATCCGTAATT 0.76031 -167 CGCGAAACGCAGGGGTTTTTGGTTGTAGCC 4 195 1 AGGGGTTTTT 0.956612 -106 TTGTAGAGAGTGGGGTTATTTTTATAGTTA 6 74 0 TGGGGTTATT 0.71123 -88 AGCGGGGATAATCCGTTATTGAACAATTTA 7 194 1 ATCCGTTATT 0.896532 -107 TCGATTGCGCAGGGGTTTTTTATTGTGTAA 10 39 1 AGGGGTTTTT 0.956612 -73 ATGGTTTCCCATCGGTTTTTTGAATTTTAA 11 28 0 ATCGGTTTTT 0.957655 -132 ATGGGAAACCATCGGTTTTTTCTTATATAA 11 46 1 ATCGGTTTTT 0.957655 -114 ********** Masking position 6 Map Score: 4.33238 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 269 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 GCTACAGAGTGTGTGAAAATTTAATTCGTA 3 115 1 GTGTGAAAAT 0.880288 -218 CAGTAAAAGGGAGTGATAATAACGATATTT 3 184 0 GAGTGATAAT 0.818659 -149 TGTGAAAACTGAGTGATAATCAACACAATA 5 13 0 GAGTGATAAT 0.818659 -50 TAAGACTTAAGTGTGAAAACTGAGTGATAA 5 24 0 GTGTGAAAAC 0.945142 -39 ATCGAAATAAGAGCAAAAACATCCACCTGA 7 90 1 GAGCAAAAAC 0.811802 -211 CAAGAGCTAAAAGTGAAAACCGTGAAATAT 8 66 1 AAGTGAAAAC 0.959781 -207 CGCGTGGCAAATGTAAAAACAAACTTAGTA 10 70 1 ATGTAAAAAC 0.821786 -42 ACTTTTATATAAGAAAAAACCGATGGTTTC 11 50 0 AAGAAAAAAC 0.762931 -110 GTAAGTTTTTAAGTAAAAACTATAACAAAC 11 78 0 AAGTAAAAAC 0.910586 -82 TTGATGAATAAAGAGAAAATTT 11 148 1 AAGAGAAAAT 0.762931 -12 ********** Masking position 6 Map Score: 5.29931 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 410 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 8 CTCTGATATGTTTAACTCCCGTTTAACAAC 4 23 0 TTTAACTCCC 0.935011 -278 TTGGCAAAGATTTACCTTCCTTTGCAAACG 4 64 1 TTTACCTTCC 0.980901 -237 ACAAGGATATTTTACCTTTCGAAATTTCTG 4 100 1 TTTACCTTTC 0.945516 -201 AGATCCGTAATTTAACTTTCGATTAGCAGA 4 126 0 TTTAACTTTC 0.854312 -175 TTAGAAAAAACTTACCTCCCCCTGTTTTAT 9 20 1 CTTACCTCCC 0.972451 -266 TCAGCAAGCACTTTCCTTCCCCTGTTTACG 9 73 1 CTTTCCTTCC 0.913076 -213 ********** Masking position 7 Map Score: 3.20831 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 126 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 ACGAGAACCCTATTTGGCTCGTTTCAAGCC 3 23 1 TATTTGGCTC 0.943553 -310 GCCGTATTTTTATTTTGCTGCAAATTGTAC 3 50 1 TATTTTGCTG 0.95983 -283 AACCGTGAAATATTTTACTGAATTAGAAGG 8 83 1 TATTTTACTG 0.787074 -190 ACATAGCAACTATATTGCTCTTAAACGTAA 8 224 0 TATATTGCTC 0.960787 -49 GGGGGCAACTTCTATTGCTCTGTCGTAAAT 9 127 1 TCTATTGCTC 0.95308 -159 AAAAAGAAATTCTTTTGCTCCAATAATTTA 9 152 0 TCTTTTGCTC 0.974293 -134 ********** Masking position 5 Map Score: 2.65023 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 95 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 AAAGGGAGTGATAATAACGATATTTGGTGACA 3 177 0 ATAATAGATA 0.709575 -156 GGTGTTAACGATAATAAAGGAGGTAGCAA 4 282 1 ATAATAGGAG 0.92907 -19 CGATCAATGAATAAACAGGAAAACAGGGGGGT 7 62 0 ATAAAAGAAA 0.956277 -239 TCGCCCCTACATAAAGATGAAGAATAGATCT 8 10 0 ATAAAAGAAG 0.955432 -263 TCGCCCCTACATAAAGATGAAGAATAGATCTC 8 146 0 ATAAAAGAAG 0.955432 -127 ATCACGGTCAATAATAAAGGAAGGCTAAT 9 267 1 ATAATAGGAA 0.930378 -19 TAGTAATAGAATAAATAAGGAAAACTT 10 95 1 ATAAAAGGAA 0.955432 -17 TTATTGATGAATAAAGAGAAAATTT 11 145 1 ATAAAAAAAA 0.709502 -15 ***** * **** Masking position 7 Map Score: 2.77356 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 112 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 CCCTTTTACTGGCTAAACCAGAAAACTTAT 3 203 1 GGCTAAACCA 0.916134 -130 GCTTAAAGATGCCTAATCCGCCAACGGCTT 3 289 1 GCCTAATCCG 0.976139 -44 TTCTGGCCGGCTAACCCGGTCACATGGG 6 9 1 GGCTAACCCG 0.988303 -153 TCGTCAGCGGGGATAATCCGTTATTGAACA 7 189 1 GGATAATCCG 0.984599 -112 CTATTTATCCTGATAATCCGTACCAGCAAC 8 117 0 TGATAATCCG 0.924532 -156 ********** Masking position 5 Map Score: 1.01519 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 201 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 CAATAAGCGCCACTATAAAAGCACA 1 6 0 CACTATAAAA 0.969812 -42 CAATTTGCAGCAAAATAAAAATACGGCTTG 3 47 0 CAAAATAAAA 0.727053 -286 CACAAGCAGTAACTATAAAAATAACCCCAC 6 65 1 AACTATAAAA 0.91565 -97 CACGCGTTTACACAATAAAAAACCCCTGCG 10 46 0 CACAATAAAA 0.94511 -66 CTATTTTAACCACTTTAAAATTCAAAAAAC 11 14 1 CACTTTAAAA 0.887963 -146 TTTAAGTAAAAACTATAACAAACTTTTATA 11 71 0 AACTATAACA 0.798762 -89 ********** Masking position 6 Map Score: 0.843898 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 58 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ********** No masking Map Score: 3.66883e-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: 3.66883e-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 AAAAAATATTGCCCTGAGCAAGGAGCCAGGGCA 2 21 0 GCCCTGGAGG 0.931093 -39 GCAAATTAAACGCGTGTCTTTTGTGAGTTTTGT 3 147 1 CGCGTGCTTG 0.956719 -186 GTCGGATTGACGCCTGTCTGCGCAAATCCAGGT 3 253 1 CGCCTGCCGC 0.874283 -80 ATATCAGAGACGCCTCTGATTTGGCAAAGATTT 4 44 1 CGCCTCGTTG 0.827912 -257 CAACCAAAAACCCCTGCGTTTCGCGATTTATTT 4 187 0 CCCCTGGTCG 0.968182 -114 ATCTCCTCATCCCATGTGACCGGGTTAGCCGGC 6 16 0 CCCATGGCGG 0.894651 -146 TTTTTCGGGCGCCCCGAGCCTTGTAGAGAGTGG 6 91 0 GCCCCGGTTG 0.79893 -71 GCGCGTGTGACCCGTCCTGAATAG 7 2 1 CGCGTGGCCG 0.949398 -299 GCAGACAAAAGGCGTGACGATGGTCGAAAATGG 7 151 1 GGCGTGCTGG 0.947456 -150 CACTTTCCTTCCCCTGTTTACGGGGGAAGGTGC 9 81 1 CCCCTGTCGG 0.910223 -205 ATGAAATGAAGCCCTGTCGATTGCGCAGGGGTT 10 23 1 GCCCTGCTTG 0.950995 -89 ATTGTGTAAACGCGTGGCAAATGTAAAAACAAA 10 60 1 CGCGTGCATG 0.890005 -52 ****** * *** Masking position 3 Map Score: 1.87248 Number of sites scoring better than the average of aligned sites = 2281 Number in coding regions = 2164 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285