AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_Glycolysis_+_PPS_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 asnS 168 asparagine tRNA synthetase #2 pncB 265 nicotinate phosphoribosyltransferase #3 glk 203 glucokinase #4 pgi 300 glucosephosphate isomerase Motif number 1 AAGCAGAATTCGCAAATGCAGCGAAAGATTTCGGAATTAAA 1 47 0 CGCATGGCAT 0.997141 -122 CTTGTCCACCCGTAAATGGGGGGATACCTATGTTACCTGGC 1 102 0 CGTATGGGAT 0.971141 -67 TTCTGCATAGCGCGATTTACGCAACAGGAATAGACTGAACA 2 43 0 CGCATTGCAT 0.993326 -223 CAGGTACAAACGCCTTTATTGCTACATTTTTATAACATACA 2 96 1 CGCTTAGCAT 0.851815 -170 TACCTTGTTTCGCAATTTATTGAACCCCGATCACACCATAT 2 167 0 CGCATTTGAT 0.835123 -99 GATGCCTTTTTGCAAGCTGGGCAAACTAAGTATCTGACCCC 3 27 0 TGCACTGCAT 0.958485 -177 AAGGCATCGCTGCAATTGGTGCTGAAACGATAAAGTAATTG 3 60 1 TGCATGGCGT 0.942096 -144 CCTCCAACACCGTTACTTGGGCAACGCGCCTCTTCTGGCCT 4 33 1 CGTATTGCAT 0.973594 -268 TTCTGGCCTGCGCTAGCGCAGGTAGTACATTTATAAATAAA 4 65 1 CGCACGGGAT 0.988384 -236 CTCAACATTACGCTAACGGCACTAAAACCATCACATTTTTC 4 211 1 CGCACGACAT 0.950213 -90 CACATTTTTCTGTGACTGGCGCTACAATCTTCCAAAGTCAC 4 242 1 TGTATGGCAT 0.955359 -59 *** * ** ** * * Masking position 21 Map Score: 10.4199 Number of sites scoring better than the average of aligned sites = 1141 Number in coding regions = 1051 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 AAGCAGAATTCGCAAATGCAGCGAAAGATTTCGG 1 54 0 CGCATGCGCA 0.985928 -115 CTTGTCCACCCGTAAATGGGGGGATACCTATGTT 1 109 0 CGTATGGGGA 0.981206 -60 ATTCCTGTTGCGTAAATCGCGCTATGCAGAATCT 2 53 1 CGTATCGGCA 0.969542 -213 GATGCCTTTTTGCAAGCTGGGCAAACTAAGTATC 3 34 0 TGCACTGGCA 0.950604 -170 AAGGCATCGCTGCAATTGGTGCTGAAACGATAAA 3 60 1 TGCATGGGCG 0.981116 -144 ATTATTTTGACTTTAGCGGAGCAGTTGAAGA 3 183 1 CTTACGGGCG 0.935515 -21 CCTCCAACACCGTTACTTGGGCAACGCGCCTCTT 4 33 1 CGTATTGGCA 0.974275 -268 TTCTGGCCTGCGCTAGCGCAGGTAGTACATTTAT 4 65 1 CGCACGCGGA 0.957123 -236 ATAAATAAAGGGTGAGCGGGGCGGTTGTCAACGA 4 97 1 GGTACGGGCG 0.968231 -204 CTCAACATTACGCTAACGGCACTAAAACCATCAC 4 211 1 CGCACGGACA 0.968835 -90 CACATTTTTCTGTGACTGGCGCTACAATCTTCCA 4 242 1 TGTATGGGCA 0.98408 -59 *** * *** ** * Masking position 5 Map Score: 12.2197 Number of sites scoring better than the average of aligned sites = 2581 Number in coding regions = 2442 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 AGCCGATTAGCTCCCTGATGATA 1 1 0 CTCCTGAATA 0.980285 -168 AGCTAATCGGCTCCCTTTTTTTACCTTTAATTC 1 22 1 CTCCTTTTTA 0.973334 -147 AATATTCTCTCTGTTAATAGTCGGAAAAA 1 150 0 CTCCTGTATA 0.995063 -19 GAAAGGCAGGCTCCCTGTAAATATCGATCTGGG 3 106 0 CTCCTGTATA 0.995063 -98 AATTCTTTCTCACACTGTAAATACCTGGGGGCA 3 153 0 CACCTGTATA 0.990828 -51 CCGCCCCGCTCACCCTTTATTTATAAATGTACT 4 88 0 CACCTTTTTA 0.95137 -213 *** **** *** Masking position 6 Map Score: 7.14637 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 CAGGGAGCTAATCGGCTCCCTTTTTTTACC 1 17 1 ATCGGCTCCC 0.949503 -152 GGTAACATAGGTATCCCCCCATTTACGGGT 1 106 1 GTATCCCCCC 0.97873 -63 CGATCACACCATATGCCACCTTTCTGGTCG 2 151 0 ATATGCCACC 0.951795 -115 CAAACTAAGTATCTGACCCCGCATAAGGAA 3 17 0 ATCTGACCCC 0.96545 -187 CGCCGGAAAGGCAGGCTCCCTGTAAATATC 3 114 0 GCAGGCTCCC 0.967248 -90 GGCGTTGTTGTTATGCCCCCAGGTATTTAC 3 140 1 TTATGCCCCC 0.983672 -64 TGAAAAATCCGCATGACCCCATCGTTGACA 4 122 0 GCATGACCCC 0.977747 -179 ********** Masking position 9 Map Score: 5.07846 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 286 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 AGGTATACTCCAGCAGTTCCTGAAGATGTTT 2 203 1 CAGCGTTCCT 0.970453 -63 GCACCAATTGCAGCGATGCCTTTTTGCAAGC 3 51 0 CAGCATGCCT 0.957105 -153 GGGGGCATAACAACAACGCCGGAAAGGCAGG 3 129 0 CAACACGCCG 0.989666 -75 TCTTCAACTGCTCCGCTAAAGTCAA 3 189 0 CAACGCTCCG 0.992987 -15 CCATCGTTGACAACCGCCCCGCTCACCCTTT 4 103 0 CAACGCCCCG 0.988104 -198 GCGGATTTTTCATCCACTCCTGGCGGTCAGT 4 140 1 CATCACTCCT 0.957746 -161 **** ****** Masking position 2 Map Score: 3.97909 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 630 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 TATAGAGTCTGGTGTTCAGTCTATTCCTGT 2 31 1 GGTGTTCAGT 0.966269 -235 TGGTGTGATCGGGGTTCAATAAATTGCGAA 2 170 1 GGGGTTCAAT 0.931244 -96 AGGTGCGCAGTAGCGTCCTCG 2 255 0 GGTGCGCAGT 0.973595 -11 ATTCCTTATGCGGGGTCAGATACTTAGTTT 3 16 1 CGGGGTCAGA 0.913927 -188 CTTTTTGCAAGCTGGGCAAACTAAGTATCT 3 33 0 GCTGGGCAAA 0.87377 -171 TTTGACTTTAGCGGAGCAGTTGAAGA 3 188 1 GCGGAGCAGT 0.969571 -16 TAAAGGGTGAGCGGGGCGGTTGTCAACGAT 4 102 1 GCGGGGCGGT 0.978405 -199 ATCCACTCCTGGCGGTCAGTAGTTCAGCTA 4 151 1 GGCGGTCAGT 0.980296 -150 ********** Masking position 4 Map Score: 3.59021 Number of sites scoring better than the average of aligned sites = 1128 Number in coding regions = 1051 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 TGGTGTTCAGTCTATTCCTGTTGCGTAAAT 2 40 1 TCTATTCCTG 0.721377 -226 GTATACTCCAGCAGTTCCTGAAGATGTTTA 2 205 1 GCAGTTCCTG 0.912397 -61 TATTGTACTAAACGCTCCTGTACGAGGACG 2 233 1 AACGCTCCTG 0.92365 -33 CCTGTACGAGGACGCTACTGCGCACCT 2 249 1 GACGCTACTG 0.91026 -17 CAGGGAGCCTGCCTTTCCGGCGTTGTTGTT 3 122 1 GCCTTTCCGG 0.932698 -82 TGTTGGAGGAGCCAGTCCTGTGATAACACC 4 12 0 GCCAGTCCTG 0.972061 -289 TGGGCAACGCGCCTCTTCTGGCCTGCGCTA 4 50 1 GCCTCTTCTG 0.971994 -251 GGATTTTTCATCCACTCCTGGCGGTCAGTA 4 142 1 TCCACTCCTG 0.98342 -159 TAGCAATACTCTTCTGATTTTGAGAA 4 285 0 TACTCTTCTG 0.81639 -16 ********** Masking position 6 Map Score: 4.73101 Number of sites scoring better than the average of aligned sites = 1450 Number in coding regions = 1335 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 8 ********** No masking Map Score: -3.23764e-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 9 ********** No masking Map Score: -3.23764e-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 10 ********** No masking Map Score: -3.23764e-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