AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i009_Nucleotide_Biosynthes_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 fixA 300 probable flavoprotein subunit, carnitine metabolism #2 fixC 50 flavoprotein; electron transport #3 yaaU 56 putative transport protein #4 yabF 107 putative NAD(P)H oxidoreductase #5 folA 191 dihydrofolate reductase type I; trimethoprim resistance #6 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #7 ygdP 300 putative invasion protein #8 HI0899_HI0900 100 HI0899: dihydrofolate reductase (folA), HI0900: glutamate 5-kinase (gamma-glutamyl kinase) (proB) #9 HI0901 80 conserved hypothetical protein Motif number 1 CATCTGACTTTCAATATTGGTGATCCATAAA 1 117 1 TCAATATTGT 0.99541 -184 AAAGAAATTTTCAATATTGTTTTATGGATCA 1 137 0 TCAATATTGT 0.99541 -164 CGCCGTGTTTTCAATATTGGTGAGGAACTTA 1 174 1 TCAATATTGT 0.99541 -127 AATCCAACTTTCAATATTGTTAAGTTCCTCA 1 194 0 TCAATATTGT 0.99541 -107 TGTGACATTTTCAATATTGGTGATTAAAGTT 1 233 1 TCAATATTGT 0.99541 -68 CTTTTCTGAATCAATATTATTGACTATAAGC 4 28 1 TCAATATTAT 0.965674 -80 TAAAAATAGCTCAAGATTGTTTCATAAATCA 9 34 0 TCAAGATTGT 0.985237 -47 ********* * Masking position 6 Map Score: 19.6772 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 18 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 2 TTTTGTTTCGGGTGAATAGAGGGCGTTTTT 1 32 1 GGTGAATAGA 0.963908 -269 TATGCTCTGTTGTGAGTAAAAAATAACATC 1 91 1 TGTGAGTAAA 0.944361 -210 TTTCAATATTGGTGAGGAACTTAACAATAT 1 182 1 GGTGAGGAAC 0.953707 -119 TTTCAATATTGGTGATTAAAGTTTTATTTC 1 241 1 GGTGATTAAA 0.8985 -60 GACTACACTTTGTGGGAAAACAAAGGCGTA 4 72 1 TGTGGGAAAA 0.739895 -36 CGAGGATGATGTTGAGGAAAATTTTATATT 5 107 0 GTTGAGGAAA 0.72158 -85 TGGATAGAGTTGTGAAGAACTACGGAATTA 7 108 0 TGTGAAGAAC 0.874785 -193 TCACCTTTTCTGTGGATAGAGTTGTGAAGA 7 120 0 TGTGGATAGA 0.901733 -181 CCACAGAAAAGGTGAATAAAAACGGCTATC 7 135 1 GGTGAATAAA 0.977086 -166 CAGAGGAAGGGGTGGATAGCCGTTTTTATT 7 149 0 GGTGGATAGC 0.939916 -152 TGTCCTTTGGTTGATAAAAGCACTGATT 9 9 1 GGTTGATAAA 0.758578 -72 ********** Masking position 8 Map Score: 7.24222 Number of sites scoring better than the average of aligned sites = 1170 Number in coding regions = 1043 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 3 TATCACATTTTTGTTTCGGGTGAATAGAGG 1 24 1 TTGTTTCGGG 0.874337 -277 TTCGTTAATTTTGATTAATAATCAGTTTGT 1 61 1 TTGATTAATA 0.756617 -240 ATTTTCAATATTGTTTTATGGATCACCAAT 1 132 0 TTGTTTTATG 0.879382 -169 GTCAATAATATTGATTCAGAAAAGAGAGAA 4 22 0 TTGATTCAGA 0.951683 -86 CTGTTTGTTTTTGTTTCATTGTAATGCGGC 5 44 1 TTGTTTCATT 0.945289 -148 ATACGAATGATTGTTTCATACTCCAGGAAG 7 255 0 TTGTTTCATA 0.969913 -46 TGATTTTTCATTGATTTAGTGATAACGTTA 8 40 0 TTGATTTAGT 0.742256 -61 TAGCTCAAGATTGTTTCATAAATCAGTGCT 9 29 0 TTGTTTCATA 0.969913 -52 ********** Masking position 5 Map Score: 4.3769 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 156 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 ATAATCAGTTTGTTATGCTCTGTTGTGAGTAA 1 78 1 TGTTATGCTG 0.990904 -223 AATTTCTTTTTGCTACGCCGTGTTTTCAATAT 1 159 1 TGCTACGCTG 0.956725 -142 TTTGTTTCATTGTAATGCGGCGAGTCCAGGGA 5 53 1 TGTAATGCCG 0.985979 -139 TAAAATTACATGTAATGCATTGACTGATAATG 7 20 1 TGTAATGCTG 0.993635 -281 GTTATTAGTGTGTAATGCCCTGCAGAGAGTGG 7 215 1 TGTAATGCTG 0.993635 -86 ******** ** Masking position 5 Map Score: 3.41551 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 16 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TTCTGTGATTGGTATCACATTTTTGTTTCG 1 12 1 GGTATCACAT 0.797275 -289 GTTAATTACAGATATCACGCCCTTTAATTT 1 272 0 GATATCACGC 0.933058 -29 TTACGCCTTTGTTTTCCCACAAAGTGTAGT 4 73 0 GTTTTCCCAC 0.911637 -35 AGGTAGCCCGCGTGATTACGC 4 97 0 GGTAGCCCGC 0.97328 -11 TGAGATTTCCCGATAAAAAAAAT 5 179 0 GATTTCCCGA 0.890179 -13 ATCTTTTAACGGTATCCGGCAACCAGCCAG 6 27 1 GGTATCCGGC 0.979375 -124 GCGCGCCGCAGGTTTCAGGCGCTCCAAAGG 6 80 0 GGTTTCAGGC 0.950429 -71 AATGCTCCGGGTTTTCCCGTAGTAATTCCG 7 86 1 GTTTTCCCGT 0.953447 -215 TGCAGAGAGTGGTTTACCGTCTTCCTGGAG 7 235 1 GGTTTACCGT 0.880386 -66 ********** Masking position 3 Map Score: 5.80388 Number of sites scoring better than the average of aligned sites = 1304 Number in coding regions = 1232 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 CCAAAATGCAGCCCTGCCAGAGTGGA 2 7 0 GCCCTGCCAG 0.989239 -44 CTGCATTTTGGCCCTGCCGCTGACAGGGAG 2 26 1 GCCCTGCCGC 0.994545 -25 TCTCTCCCTGGACTCGCCGCATTACAATGA 5 59 0 GACTCGCCGC 0.970856 -133 AGAGAGCGTGGACTCGCCAGCAGAATATAA 5 84 1 GACTCGCCAG 0.942874 -108 ATTGAAATGCGCGCCGCAGGTTTCAGGCGC 6 88 0 GCGCCGCAGG 0.970268 -63 AGTGTGTAATGCCCTGCAGAGAGTGGTTTA 7 221 1 GCCCTGCAGA 0.958573 -80 ********** Masking position 6 Map Score: 2.98954 Number of sites scoring better than the average of aligned sites = 1132 Number in coding regions = 1081 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 AAAAAATAACATCTGACTTTCAATATTGGTGATC 1 108 1 ACCTTTCAAT 0.941432 -193 GCGTAGCAAAAAGAAATTTTCAATATTGTTTTAT 1 143 0 AGTTTTCAAT 0.959817 -158 TTTTTGCTACGCCGTGTTTTCAATATTGGTGAGG 1 165 1 GCTTTTCAAT 0.9839 -136 ACGCAGATAAATCCAACTTTCAATATTGTTAAGT 1 200 0 ACCTTTCAAT 0.941422 -101 TTATCTGCGTGTGACATTTTCAATATTGGTGATT 1 224 1 GGTTTTCAAT 0.9839 -77 ATATTCACGCGGCTTATAGTCAATAATATTGATT 4 36 0 GCTAGTCAAT 0.855952 -72 GAAACCTGCGGCGCGCATTTCAATCGCTGTTCTC 6 94 1 GGATTTCAAT 0.937797 -57 GCACATAACTGTGAGTTATTCAATTGTTATTAGT 7 190 1 GGTATTCAAT 0.957214 -111 * * ******** Masking position 12 Map Score: 3.90987 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 75 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GGCGTTTTTTCGTTAATTTTGATTAATAATC 1 53 1 CGTTATTTTG 0.918817 -248 AATATTGAAAATTTCTTTTTGCTACGCCGTG 1 150 1 ATTTTTTTTG 0.788566 -151 ATATCACGCCCTTTAATTTTGAAATAAAACT 1 260 0 CTTTATTTTG 0.950726 -41 CTCTGGCAGGGCTGCATTTTGGCCCTGCCGC 2 15 1 GCTGATTTTG 0.953306 -36 GGTTATTCCTGTTTTTTGCAATGAGAGT 3 39 0 CCTGTTTTTG 0.940045 -18 ACAGCTAACTGTTTGTTTTTGTTTCATTGTA 5 36 1 GTTTTTTTTG 0.936781 -156 CGTATATAAAGCTTTATTTTGAGGTAGTCCG 7 280 1 GCTTATTTTG 0.968092 -21 **** ****** Masking position 7 Map Score: 2.11714 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 229 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 9 TGTGATTGGTATCACATTTTTGTTTCGGGT 1 15 1 ATCACATTTT 0.741985 -286 AATTACAGATATCACGCCCTTTAATTTTGA 1 269 0 ATCACGCCCT 0.94548 -32 TGAATATATGACTACACTTTGTGGGAAAAC 4 63 1 ACTACACTTT 0.812178 -45 AGCCCGCGTGATTACGCCTTTGTTTTCCCA 4 84 0 ATTACGCCTT 0.872753 -24 AGTGACGTAAATCACACTTTACAGCTAACT 5 16 1 ATCACACTTT 0.949152 -176 TGCTGGCGAGTCCACGCTCTCTCCCTGGAC 5 76 0 TCCACGCTCT 0.935873 -116 TCGACGACGGTTTACGCTTTACGTATAGTG 5 143 1 TTTACGCTTT 0.860564 -49 TGTGCTATTATTCGCACCTTTGGAGCGCCT 6 64 1 TTCGCACCTT 0.734501 -87 GCCGTTTTTATTCACCTTTTCTGTGGATAG 7 131 0 TTCACCTTTT 0.667363 -170 AAAACGGCTATCCACCCCTTCCTCTGTTTA 7 153 1 TCCACCCCTT 0.919288 -148 AAGACGGTAAACCACTCTCTGCAGGGCATT 7 228 0 ACCACTCTCT 0.768691 -73 ********** Masking position 10 Map Score: 3.72709 Number of sites scoring better than the average of aligned sites = 1339 Number in coding regions = 1204 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 10 ********** No masking Map Score: -3.48633e-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 11 ********** No masking Map Score: -3.48633e-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 12 ********** No masking Map Score: -3.48633e-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