AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00053_ecoli_reg_100.orf -o00053_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e 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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #2 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #3 rspA 205 starvation sensing protein #4 gatD 47 galactitol-1-phosphate dehydrogenase #5 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #6 gatZ 28 putative tagatose 6-phosphate kinase 1 #7 gatY 197 tagatose-bisphosphate aldolase 1 #8 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #9 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #10 cvpA 165 membrane protein required for colicin V production #11 pdxB 98 erythronate-4-phosphate dehyrogenase #12 b2789 300 putative transport protein #13 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) Motif number 1 TAAAGAATGTCGCCAGAAATAAACGGGCATACGGC 2 183 1 CGAAAAAACG 0.986581 -92 CAACCATTCACAGCGCAAATATACGCCTTTTTTTG 3 85 1 CAGAAAAACG 0.977394 -121 TCACGACAAGCGATGCAAGGAATCGAAC 3 188 1 CGGAAGATCG 0.942274 -18 ATGCCGGATGCGGTGTAAACATACGTGGCAGTGCT 7 13 0 CGGAAAAACG 0.991574 -185 ACACCGCATCCGGCATAAAAACACGCGCACTTTGC 7 32 1 CGAAAAAACG 0.986581 -166 TCGAGGAGTGAAAGGCAAAAAAACGGCCTCCCGAT 7 79 0 AAGAAAAACG 0.964302 -119 TATATTTTGAAATCGAAAACAAACGACAGGAT 7 176 1 AAGAAAAACG 0.964302 -22 ATGTGGCTTAACGAGGAAAAAGACGT 9 21 1 ACGAAAAACG 0.924063 -16 GATGCCGCAAAGGCATAAAAAGTCGATGGCGTTGA 10 22 1 AGAAAAATCG 0.91934 -144 CGCATTCTAACAGAAAAAGAAAACGTTTGCGTAGG 10 101 0 CAAAAGAACG 0.937894 -65 CGAAGATTTCAGGTATAAGGATACGTA 11 3 0 AGAAAGAACG 0.96252 -96 TGCTATTGCCAGATATAAACACGCGCCGTATTCGG 12 168 1 AGAAAAAGCG 0.905482 -133 ** * *** * *** Masking position 8 Map Score: 16.9352 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 229 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 AATAAGTTGCGCTGTACTGTGCGCGCAACGACATTTTGT 1 28 1 GTACGCGCGC 0.988912 -49 GTTGCATCAAGGCGGCAAGTGAGCGAATCCCGATGAGCT 2 75 1 GGCAGAGCGC 0.916049 -200 GAAATAAACGGGCATACGGCCCGGGGATCTCTGCGCCCT 2 198 1 GTACGCGGGC 0.966315 -77 ACTTTGCTACGGCTTCCCTATCGGGAGGCCGTTTTTTTG 7 60 1 GTCCTCGGGC 0.994181 -138 TTGCAAGTCAGGGTGCCAGACCGGCACCCTCAGCGAAGG 8 13 0 GGCCGCGGCC 0.533991 -82 AAGTCTGCCTGCAAGTCTGACAGGGCAACTATTT 8 71 1 GGTCGAGGGC 0.906231 -24 TTTGCGTAGGGATTTCCTTCCCGCGCATCAATAAAAATG 10 72 0 GTCCTCGCGC 0.988163 -94 TTTACGCCCTGTCATCCTGTTCGGGGCGCATTCTAACAG 10 123 0 GTCCGCGGGC 0.994407 -43 ATCTTCGCAAGTATGCCTGGCCGCGAGATTATGGCACAC 11 31 1 GGCCGCGCGT 0.98353 -68 AGTATAAAAAGCGCGCCATAGCGGCTCACCGTGCAACAA 12 130 0 GGCCTCGGCC 0.859916 -171 * *** * **** * Masking position 13 Map Score: 15.1643 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 525 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 CATTGCGCTTACCCGGCTTACAGAACAAAA 2 14 0 ACCCGGCTTA 0.918424 -261 AGCGCAATGCGCCCGGCAATCTATACACAA 2 35 1 GCCCGGCAAT 0.898412 -240 CGCACCTGCCATTTAACAAGGAA 6 4 1 ACCTGCCATT 0.895641 -25 GTGTAAACATACGTGGCAGTGCTAT 7 6 0 ACGTGGCAGT 0.853837 -192 TTTACACCGCATCCGGCATAAAAACACGCG 7 29 1 ATCCGGCATA 0.882013 -169 GTGCTCTGAGATGTGGCTTAACGAGGAAAA 9 11 1 ATGTGGCTTA 0.764525 -26 TAATCTCGCGGCCAGGCATACTTGCGAAGA 11 32 0 GCCAGGCATA 0.816708 -67 AACCGGACAAGTGTGCCATAATCTCGCGGC 11 50 0 GTGTGCCATA 0.787658 -49 AGTATAAAAAGCGCGCCATAGCGGCTCACC 12 139 0 GCGCGCCATA 0.950241 -162 GCGTGTTTATATCTGGCAATAGCAGTATAA 12 162 0 ATCTGGCAAT 0.612932 -139 AGATATAAACACGCGCCGTATTCGGCGAAC 12 178 1 ACGCGCCGTA 0.907761 -123 TCCAGAGTGAGCGTGGCTAACGCGAATTTT 12 268 1 GCGTGGCTAA 0.813655 -33 CCACGTAAACACGTGGCGTTTTTGGCATAA 13 18 0 ACGTGGCGTT 0.950059 -222 CCACGTGTTTACGTGGCGTTTTGCTTTTAT 13 32 1 ACGTGGCGTT 0.950059 -208 AACATCGCCAGCGCGGCATTAAGATTACAG 13 64 0 GCGCGGCATT 0.978196 -176 ********** Masking position 5 Map Score: 13.2452 Number of sites scoring better than the average of aligned sites = 3553 Number in coding regions = 3337 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 4 AGCCGCCTCTGCCTTGGCTGCGTTCGCTCCCCCGAAT 2 128 0 GCTGCGGTGC 0.988249 -147 TACTTGTATGGTAGTAGCTCAGTTGCGTAGATTTCAT 3 148 1 GTTGCCGTCG 0.931307 -58 CGATAGGGAAGCCGTAGCAAAGTGCGCGTGTTTTTAT 7 46 0 GCTGCAGTGC 0.987235 -152 TGCCTTCGCTGAGGGTGCCGGTCTGGCA 8 2 1 GCTGCGGGGC 0.986052 -93 CTTGCAGGCAGACTTTGCAGGATTTCGGCGGGAGTTG 8 49 0 GATGCGATCG 0.779223 -46 GACTTTTTATGCCTTTGCGGCATCGGGCAATGCGT 10 9 0 GCTGCGATGG 0.989778 -157 CCCGATTTTGGCATTAGCCCTGGACGGTGGAATCCAC 12 68 0 GCTGCCGGGG 0.991048 -233 TTAATGTTGTGTTGTTGCACGGTGAGCCGCTATGGCG 12 119 1 GTTGCCGTGC 0.971687 -182 TTTTTATAGGTCGTTCGCCGAATACGGCGCGTGTTTA 12 183 0 TCTGCGATGG 0.911708 -118 TCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCCTG 13 70 1 GCTGCAGTGG 0.991325 -170 ** * ** * ** ** Masking position 5 Map Score: 10.6107 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 805 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 ATCAGATATATGCAGTTTGTGAACGTCAGG 2 234 0 TGCAGTTTGT 0.670492 -41 TGAAATAGAATACCTTTTGTCAGCTGACAC 3 47 0 TACCTTTTGT 0.638897 -159 TATTCTATTTCATCTTTTGTCAACCATTCA 3 65 1 CATCTTTTGT 0.466568 -141 CGCAAATATACGCCTTTTTTTGTGATCACT 3 98 1 CGCCTTTTTT 0.956635 -108 GTGATCACTCCGGCTTTTTTCGATCTTTAT 3 119 1 CGGCTTTTTT 0.919151 -87 CCTATCGGGAGGCCGTTTTTTTGCCTTTCA 7 76 1 GGCCGTTTTT 0.917862 -122 ATTTTCATATTGTCGTTTTTGTGATCGTTA 7 117 1 TGTCGTTTTT 0.947242 -81 ATCCTGTCGTTTGTTTTCGATTTC 7 184 0 TGTCGTTTGT 0.929498 -14 ACGTCTTTTTCCTCGTTAAGC 9 26 0 CGTCTTTTTC 0.617759 -11 ATTTTTTCAGCGCCATTTTTATTGATGCGC 10 59 1 CGCCATTTTT 0.844778 -107 GGGTGTTTTTTGCCGTTTTTATAGGTCGTT 12 205 0 TGCCGTTTTT 0.976783 -96 CGTAAACACGTGGCGTTTTTGGCATAAGAC 13 15 0 TGGCGTTTTT 0.955912 -225 CGTGTTTACGTGGCGTTTTGCTTTTATATC 13 35 1 TGGCGTTTTG 0.78823 -205 ********** Masking position 6 Map Score: 10.7344 Number of sites scoring better than the average of aligned sites = 1757 Number in coding regions = 1497 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 249 Fraction of orfs with sites within 600 bp upstream = 0.0399936 Motif number 6 ATCGGGATTCGCTCACTTGCCGCCTTGATGC 2 78 0 GCCACTTGCC 0.754496 -197 ATCCCGATGAGCTTACTCAGGTAAGTGATTC 2 101 1 GCTACTCAGG 0.769661 -174 CATCCTTCAAGCCGCCTCTGCCTTGGCTGCG 2 143 0 GCGCCTCTGC 0.952563 -132 GGGGATCTCTGCGCCCTGACGTTCACAAACT 2 220 1 GCCCCTGACG 0.950645 -55 GGGGATAACCTCCCCCTCAGGTAAAAA 4 7 0 TCCCCTCAGG 0.814647 -41 ATAAAAACACGCGCACTTTGCTACGGCTTCC 7 46 1 GCCACTTTGC 0.954956 -152 TGCCAGACCGGCACCCTCAGCGAAGGCA 8 8 0 GCCCCTCAGC 0.985689 -87 TGCCGGTCTGGCACCCTGACTTGCAACTCCC 8 26 1 GCCCCTGACT 0.786821 -69 AGACTTGCAGGCAGACTTTGCAGGATTTCGG 8 58 0 GCGACTTTGC 0.822992 -37 CTGTTAGAATGCGCCCCGAACAGGATGACAG 10 123 1 GCCCCCGAAC 0.74248 -43 CGCCATAGCGGCTCACCGTGCAACAACACAA 12 125 0 GCCACCGTGC 0.904074 -176 CGTTAGCCACGCTCACTCTGGACTGCGACAT 12 259 0 GCCACTCTGG 0.966664 -42 ** ******** Masking position 6 Map Score: 6.83846 Number of sites scoring better than the average of aligned sites = 1162 Number in coding regions = 1066 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 7 TGCGCGCACAGTACAGCGCAACTTATTTTG 1 25 0 GTACAGCGCA 0.921349 -52 GGCCCGGGGATCTCTGCGCCCTGACGTTCA 2 215 1 TCTCTGCGCC 0.940673 -60 TGTCAACCATTCACAGCGCAAATATACGCC 3 82 1 TCACAGCGCA 0.989837 -124 CCACGTATGTTTACACCGCATCCGGCATAA 7 20 1 TTACACCGCA 0.863034 -178 AGACCGGCACCCTCAGCGAAGGCA 8 5 0 CCTCAGCGAA 0.916641 -90 TTAAGCCACATCTCAGAGCAC 9 2 0 TCTCAGAGCA 0.97278 -35 TTGAATATTTTTTCAGCGCCATTTTTATTG 10 53 1 TTTCAGCGCC 0.971898 -113 AATGCATGCTCTCAGAGAAAATTATTAGC 13 221 0 TCTCAGAGAA 0.890997 -19 ********** Masking position 4 Map Score: 4.2857 Number of sites scoring better than the average of aligned sites = 972 Number in coding regions = 912 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 TATATCTGATAGACGTGAAACAGGAGTCAT 2 254 1 AGACGTGAAA 0.93959 -21 GCTTGTCGTGATGCATGAAATCTACGCAAC 3 169 0 ATGCATGAAA 0.703068 -37 AAATTATTCGAGGAGTGAAAGGCAAAAAAA 7 91 0 AGGAGTGAAA 0.973588 -107 GATGCCGCAAAGGCATAAAAAGTCGATGGC 10 22 1 AGGCATAAAA 0.82628 -144 ATTGATGCGCGGGAAGGAAATCCCTACGCA 10 79 1 GGGAAGGAAA 0.883238 -87 CAGGATGACAGGGCGTAAAATCGTGGGACA 10 143 1 GGGCGTAAAA 0.885164 -23 TCCACTTCACGGAAATGAAAACAAGAACAA 12 43 0 GGAAATGAAA 0.835307 -258 GCGAATTTTCAGGAGTGCAACA 12 289 1 AGGAGTGCAA 0.895968 -12 ACCTTTATTCAGAAGGGAAAGTCCGTTCCA 13 173 0 AGAAGGGAAA 0.855182 -67 ********** Masking position 9 Map Score: 3.02646 Number of sites scoring better than the average of aligned sites = 941 Number in coding regions = 809 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 9 ********** No masking Map Score: 1.50878e-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: 1.50878e-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 TTACATGTTTTTAACAAAATAAGTTGCGCTG 1 10 1 TTAACAAATA 0.857694 -67 ATCCCTCTGTAACAATAAAAAGGACTATT 5 8 1 TTAACAAAAA 0.966697 -23 GCACCTGCCATTTAACAAGGAAAAAAC 6 12 1 TTAACAAGAA 0.951306 -17 TATCTCGATATTTAAAAACAAATAATTTCATT 7 145 1 TTAAAAAAAA 0.887887 -53 CGGGGCGCATTCTAACAGAAAAAGAAAACGTT 10 109 0 TTAACAGAAA 0.951306 -57 AGATTACAGATATAAAAGCAAAACGCCACGTA 13 41 0 TTAAAAGAAA 0.842007 -199 TTAGCAGAAGTATAACCACGAAGACCTTTATT 13 194 0 TTAACCAGAA 0.857373 -46 * ****** *** Masking position 5 Map Score: 0.496406 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 27 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 ********** No masking Map Score: 1.50878e-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 13 ********** No masking Map Score: 1.50878e-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: 1.50878e-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