AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inagC_ecoli_opreg_300.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 Motif number 1 AATACGGCTTGAAACGAGCCAAATAGGGTTCTCGT 3 23 0 GACGCCAATA 0.987649 -310 TTTAATTTGCGATACGAATTAAATTTTCACACACT 3 122 0 GACGTTAATT 0.986947 -211 ACTCACAAAAGACACGCGTTTAATTTGCGATACGA 3 140 0 GACGTTAATT 0.986956 -193 TGCCAAATCAGAGGCGTCTCTGATATGTTTAACTC 4 35 0 GACGTCGATA 0.987663 -266 GTCCACAATCGAATCGATTCAGATAAGGGCTACAA 4 217 0 GACGTCGATA 0.987413 -84 GCGCGTGTGACCCGTCCTGAATAGCGTTCACAT 7 9 1 GACGCTAATA 0.985131 -292 TTTTCAAGGTGAAGCGGTTTAAATTCGTTCTCAAA 7 259 1 GACGTTAATT 0.986956 -42 ** ** ** **** Masking position 13 Map Score: 7.08444 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 22 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 TTATTATCACTCCCTTTTACTGGCTAAACC 3 192 1 TCCCTTTTAC 0.976834 -141 TCTGCGCAAATCCAGGTTACGCTTAAAGAT 3 269 1 TCCAGGTTAC 0.977507 -64 GCCAACGGCTTACATTTTACTTATTGAGGT 3 308 1 TACATTTTAC 0.724438 -25 TATGTTTAACTCCCGTTTAACAACCATGGA 4 17 0 TCCCGTTTAA 0.902452 -284 AGGTAAAATATCCTTGTCACATTCGTTTGC 4 87 0 TCCTTGTCAC 0.948038 -214 TGTACTTCTCCTGTTTACGTAAGACTTA 5 45 0 TCCTGTTTAC 0.981373 -18 TGGCCGGCTAACCCGGTCACATGGGATGAG 6 14 1 ACCCGGTCAC 0.898842 -148 CCCCCTGTTTTCCTGTTTATTCATTGATCG 7 64 1 TCCTGTTTAT 0.854725 -237 TTATCCTCTGTCCATTTCACGATGAAAAAA 7 221 1 TCCATTTCAC 0.956746 -80 ********** Masking position 7 Map Score: 7.09589 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 433 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 TTGTTATCCCTGCCCTGGCTCCT 2 3 1 GTTATCCCTC 0.982551 -57 CTTATTCCCCCTACGAGAACCCTA 3 4 1 ATTCCCCCTC 0.911253 -329 AAATATCGTTATTATCACTCCCTTTTACTGG 3 184 1 ATTATCACTC 0.96388 -149 CTTTATTATCGTTAACACCTCAACGTGCCAG 4 270 0 GTTAACACCC 0.912082 -31 TATTGTGTTGATTATCACTCAGTTTTCACAC 5 13 1 ATTATCACTA 0.723461 -50 GGGAGATTATGTTATCTCCTCATCCCATGTG 6 31 0 GTTATCTCCC 0.918137 -131 GAGATAACATAATCTCCCTCCCACAAGCAGT 6 44 1 AATCTCCCTC 0.913384 -118 TAACTATAAAAATAACCCCACTCTCTACAAG 6 74 1 AATAACCCCC 0.910458 -88 TCAATAACGGATTATCCCCGCTGACGAAAGC 7 185 0 ATTATCCCCC 0.98875 -116 ********* * Masking position 3 Map Score: 5.1804 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 378 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 CAATATTTTTTAAAATCGGGGGTCAGA 2 43 1 TAAAATCGGG 0.956162 -17 GCAGCAAAATAAAAATACGGCTTGAAACGA 3 41 0 AAAAATACGG 0.956994 -292 TTTTGAATGATAAAATAAGTTTTCTGGTTT 3 217 0 TAAAATAAGT 0.749835 -116 TTATCATTCAAAAAATCAGGTCGGATTGAC 3 234 1 AAAAATCAGG 0.963382 -99 AATCGAAAGTTAAATTACGGATCTTCATCA 4 132 1 TAAATTACGG 0.932756 -169 GGGGCGCCCGAAAAAACGGGCATACAGGTT 6 109 1 AAAAAACGGG 0.796282 -53 ACCTGACGCTTAAATTAAGGTACTGCCTTA 7 114 1 TAAATTAAGG 0.943604 -187 TTGTCTGCAGAAAATTAAGGCAGTACCTTA 7 129 0 AAAATTAAGG 0.943604 -172 ********** Masking position 4 Map Score: 4.65315 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 229 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 ATTCAAAAAATCAGGTCGGATTGACGCCTGT 3 239 1 TCAGGCGGAT 0.994008 -94 TTCTGGCCGGCTAACCCGGTCA 6 2 1 TCTGGCGGCT 0.97175 -160 TGAACGCTATTCAGGACGGGTCACACGCGC 7 10 0 TCAGGCGGGT 0.996112 -291 AAACAGGAAAACAGGGGGGTTTTATATCAGC 7 51 0 ACAGGGGGTT 0.923841 -250 GGCGCTTTCGTCAGCGGGGATAATCCGTTAT 7 182 1 TCAGCGGGAT 0.952108 -119 CAAATTACAGTCAGGACGCGT 7 290 1 TCAGGCGCGT 0.983281 -11 ***** ***** Masking position 11 Map Score: 3.68551 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 138 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 GAGCAAGGAGCCAGGGCAGGGATAACAA 2 9 0 CCAGGGCAGG 0.885996 -51 GGCTCCTTGCTCAGGGCAATATTTTTTAAA 2 27 1 TCAGGGCAAT 0.903948 -33 ATTCAAAAAATCAGGTCGGATTGACGCCTG 3 239 1 TCAGGTCGGA 0.922261 -94 TCTTACGTAAACAGGAGAAGTACA 5 49 1 ACAGGAGAAG 0.748364 -14 TGAACGCTATTCAGGACGGGTCACACGCGC 7 11 0 TCAGGACGGG 0.984962 -290 GGGTTTTATATCAGCAGGATCTATGTGAAC 7 36 0 TCAGCAGGAT 0.849011 -265 AAACAGGAAAACAGGGGGGTTTTATATCAG 7 52 0 ACAGGGGGGT 0.953931 -249 AATTTAAGCGTCAGGTGGATGTTTTTGCTC 7 100 0 TCAGGTGGAT 0.918504 -201 GGCGCTTTCGTCAGCGGGGATAATCCGTTA 7 182 1 TCAGCGGGGA 0.903644 -119 CAAATTACAGTCAGGACGCGT 7 290 1 TCAGGACGCG 0.9376 -11 ********** Masking position 3 Map Score: 4.41265 Number of sites scoring better than the average of aligned sites = 1532 Number in coding regions = 1384 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 7 TATTTGGCTCGTTTCAAGCCGTATTTTTATTTT 3 33 1 GTTTCGCGTA 0.956887 -300 GATAAAATAAGTTTTCTGGTTTAGCCAGTAAAA 3 206 0 GTTTTGTTTA 0.975956 -127 AAACCCCTGCGTTTCGCGATTTATTTTAGATAT 4 180 0 GTTTCGTTTA 0.964681 -121 AAACGCAGGGGTTTTTGGTTGTAGCCCTTATCT 4 199 1 GTTTTGTGTA 0.964681 -102 TTATCACTCAGTTTTCACACTTAAGTCTTACGT 5 24 1 GTTTTCCTTA 0.962434 -39 AAACCCCCCTGTTTTCCTGTTTATTCATTGATC 7 60 1 GTTTTTTTTA 0.886079 -241 TCAGGTGGATGTTTTTGCTCTTATTTCGATCAA 7 87 0 GTTTTCCTTA 0.962434 -214 ***** * **** Masking position 13 Map Score: 3.36022 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 55 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 AAATTGTACTGCCGATGTTCTGTAATCAGATTGTT 3 71 1 GCGAGTCTAA 0.983558 -262 ACACTCTGTAGCAGATGATCTAACAATCTGATTAC 3 92 0 GCGAGTCACA 0.976912 -241 GATATTTGGTGACAAAACTCACAAAAGACACGCGT 3 156 0 GAAAATCAAA 0.801163 -177 CTTTCGATTAGCAGAAATTTCGAAAGGTAAAATAT 4 106 0 GCGAATTAAA 0.910978 -195 TATTTTATGTGATGAAGATCCGTAATTTAACTTTC 4 136 0 GAGAGTCTAA 0.980213 -165 TTCGATTGTGGACGACGATTCAAAAATACATCTGG 4 239 1 GAGAGTTAAA 0.968812 -62 CAAAAGGCGTGACGATGGTCGAAAATGGCGCTTTC 7 156 1 GAGAGTCAAA 0.991295 -145 ** ** * ** *** Masking position 5 Map Score: 1.23077 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 199 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 AACTCACAAAAGACACGCGTTTAATTTGCG 3 146 0 AGACACGCGT 0.993056 -187 GGATTTGCGCAGACAGGCGTCAATCCGACC 3 252 0 AGACAGGCGT 0.981794 -81 TAAACATATCAGAGACGCCTCTGATTTGGC 4 39 1 AGAGACGCCT 0.981794 -262 TTTCGACCATCGTCACGCCTTTTGTCTGCA 7 150 0 CGTCACGCCT 0.971065 -151 ********** Masking position 5 Map Score: 0.420915 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 18 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 AATAAGCGCCACTATAAAAGCACA 1 5 0 ACTATAAAAG 0.891359 -43 TGAGGTGTTAACGATAATAAAGGAGGTAGC 4 279 1 ACGATAATAA 0.925778 -22 ACAAGCAGTAACTATAAAAATAACCCCACT 6 66 1 ACTATAAAAA 0.94795 -96 TTGACCGACAACGATATAAATCGGAATCAA 6 137 1 ACGATATAAA 0.925775 -25 TGTCCATTTCACGATGAAAAAAATGTAGTT 7 229 1 ACGATGAAAA 0.948683 -72 ********** Masking position 5 Map Score: 0.342069 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 80 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 AGACACGCGTTTAATTTGCGATACGAATTA 3 136 0 TTAATTTGCG 0.891433 -197 TCTGATATGTTTAACTCCCGTTTAACAACC 4 22 0 TTAACTCCCG 0.942368 -279 TGGCAAAGATTTACCTTCCTTTGCAAACGA 4 65 1 TTACCTTCCT 0.926077 -236 CAAGGATATTTTACCTTTCGAAATTTCTGC 4 101 1 TTACCTTTCG 0.971707 -200 GATCCGTAATTTAACTTTCGATTAGCAGAA 4 125 0 TTAACTTTCG 0.976429 -176 AGGTACTGCCTTAATTTTCTGCAGACAAAA 7 131 1 TTAATTTTCT 0.825478 -170 ********** Masking position 6 Map Score: 1.68918 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 124 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 ********** No masking Map Score: 7.41397e-13 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 13 ********** No masking Map Score: 7.41397e-13 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: 7.41397e-13 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