AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i314_ecoli_bsub_300.orf -o314_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 trpE 215 anthranilate synthase #2 aroB 61 3-dehydroquinate synthase #3 aroF 69 chorismate synthase #4 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #5 ndk 115 nucleoside diphosphate kinase #6 gerCA 162 heptaprenyl diphosphate synthase component I #7 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #8 mtrA 187 GTP cyclohydrolase I #9 hbs 300 non-specific DNA-binding protein HBsu Motif number 1 AGAACAGCTTAGAAATACACAAGAGTGTGTATAAAGCAATTAGAA 1 18 1 AGAAATTAAA 0.991907 -198 AGTTGAGCTGAGACATTATGTTTATTCTACCCAAAAGAAGTCTTT 1 102 1 AGACATTAAA 0.981378 -114 ACCGCATTAGAGAAAATGTGGAGAATATGAGAAAACTGTCGAGGG 2 20 1 AGAAATTAAA 0.991907 -42 TAAAATCAGCTGAAAAGCTGATTTTTTTATTGAAACAATACAATT 4 146 1 TGAAATTAAA 0.945193 -91 TCCGGGGCGGAGAAATTTCTTAATATCTACAAAAA 5 1 0 AGAAATTAAA 0.991907 -115 ACATAGATTAAGAAATAAATGTGAATTTGGGGACAAGGGTGATAT 6 126 1 AGAAATTACA 0.96235 -37 AAAGCCCCTTAGAAAGGGGCTTTTCTGTGAAGAAATAAAGTGTAT 8 45 0 AGAAATTAAA 0.991907 -143 CTCTACATACAGAAATTCTTCACTTTGTTGGACAAACATTCCTCA 9 120 1 AGAAATTCAA 0.966257 -181 AGTAAGAGAAAGACAATTAAACGGCTTTTTAAGAAAAACTGCACT 9 166 0 AGACATTGAA 0.924886 -135 AGACAGGTTTAGAATCAGACTGAACTGTGAAGAAATGATAATAAA 9 229 1 AGAATTTAAA 0.945193 -72 ***** * * *** Masking position 16 Map Score: 11.2015 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 15 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 TAGAATGAGTTGAGTTAGAGAATAGGGTAGCA 1 58 1 TGGTAGAGAA 0.983412 -158 TAGAGAATAGGGTAGCAGAGAATGAGTTTAGT 1 73 1 GGAGAGAGAA 0.973978 -143 ATGAGAAGATGGCATGAGAGGATAAAATACTA 1 168 0 GGATAGAGGA 0.889769 -48 CTTGCCATAAGGAGTGAGAGCA 1 204 1 GGGTAGAGCA 0.966225 -12 TCAAATTGACCGCATTAGAGAAAATGTGGAGA 2 12 1 CGATAGAGAA 0.963373 -50 TTAATCAATCCGGGGCGGAGAAATTTCTTAAT 5 22 0 CGGGGGAGAA 0.986284 -94 TACATAATGATGGGGTGGAGAAT 5 103 1 TGGGGGAGAA 0.978601 -13 TAATGATACCTGCGTAAGCGAATGAAAAGATA 6 86 1 TGGTAGCGAA 0.932663 -77 AAAATGAGAGCAAGTAAGAGAAAGACAATTAA 9 191 0 CAGTAGAGAA 0.890642 -110 TATCCTTTTGGGAGGAGGTGAAAGGC 9 285 1 GGGGGGTGAA 0.937064 -16 ** ** ****** Masking position 12 Map Score: 7.84111 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 560 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 ATTCTAATTGCTTTATACACACTCTTGTGT 1 34 0 CTTTATACAC 0.620655 -182 TTCTCTGCTACCCTATTCTCTAACTCAACT 1 65 0 CCCTATTCTC 0.886201 -151 GCTCAACTAAACTCATTCTCTGCTACCCTA 1 80 0 ACTCATTCTC 0.758728 -136 TCCTCTCATGCCATCTTCTCATTCTCCTTG 1 178 1 CCATCTTCTC 0.961046 -38 CATATTCTCCACATTTTCTCTAATGCGGTC 2 19 0 ACATTTTCTC 0.704546 -43 GACAGTTTTCTCATATTCTCCACATTTTCT 2 30 0 TCATATTCTC 0.734221 -32 GACTTCTTCTCCCTTCATCGC 3 59 0 ACTTCTTCTC 0.954996 -11 CCATTCAACCCTTTATTCACTTTAATGTAA 4 81 0 CTTTATTCAC 0.93893 -156 ACCCTTGTCCCCAAATTCACATTTATTTCT 6 136 0 CCAAATTCAC 0.740784 -27 CATACACGATCTATATTCACAA 8 3 0 CTATATTCAC 0.917818 -185 CATACACTTTATTTCTTCACAGAAAAGCCC 8 44 1 ATTTCTTCAC 0.917542 -144 TACATACAGAAATTCTTCACTTTGTTGGAC 9 123 1 AATTCTTCAC 0.732989 -178 GTTTATTATCATTTCTTCACAGTTCAGTCT 9 245 0 ATTTCTTCAC 0.917542 -56 ********** Masking position 6 Map Score: 8.20547 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 724 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 GTGTGTATAAAGCAATTAGAATGAGTTGAGTTAGAGA 1 42 1 AGATTTGGTT 0.947521 -174 ACCCAAAAGAAGTCTTTCTTTTGGGTTTATTTGTTAT 1 130 1 AGTTTTGGTT 0.980127 -86 TAACGCCGCCGGTTTTTGTTCTGTTTTGTAAAGGTTT 4 46 1 GGTTTTGTTT 0.987626 -191 TAAAAAAATCAGCTTTTCAGCTGATTTTAGATCGTTG 4 138 0 AGTTTTGTTT 0.980514 -99 TGTTTTATCAGGAAATTGTATTGTTTCAATAAAAAAA 4 167 0 GGATTTGTTC 0.88585 -70 TTCCTGACAGGGCATTCACTTTGCTTTTAGCGGGGCA 8 111 1 GGTTCTGTTT 0.954952 -77 TTGCTCGTCAAGGATTTAAGGTGATTTACCGAACGAA 9 37 0 AGTTTTGTTT 0.980514 -264 TGCTTGATATGGCTTTTTATATGTGTTACTCTACATA 9 92 1 GGTTTTGGTT 0.987378 -209 ** *** ** *** Masking position 6 Map Score: 6.2887 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 48 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 ATCAGCTTTTCAGCTGATTTTAGATCGTTG 4 138 0 CAGCTGATTT 0.854901 -99 ATCAGCTGAAAAGCTGATTTTTTTATTGAA 4 150 1 AAGCTGATTT 0.956864 -87 TTTGGGGACAAGGGTGATATTT 6 151 1 AGGGTGATAT 0.882098 -12 TAAAGATAGAGGGTGCTATAA 7 10 1 AGGGTGCTAT 0.922281 -12 GCCCCTTAGAAAGGGGCTTTTCTGTGAAGA 8 57 0 AAGGGGCTTT 0.982173 -131 GCCCCTTTCTAAGGGGCTTTTCATATTTCA 8 70 1 AAGGGGCTTT 0.982173 -118 TCAAGGATTTAAGGTGATTTACCGAACGAA 9 37 0 AAGGTGATTT 0.973027 -264 AAAGACAATTAAACGGCTTTTTAAGAAAAA 9 173 0 AAACGGCTTT 0.793555 -128 ********** Masking position 8 Map Score: 6.84952 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 258 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 ATTTTCTCTAATGCGGTCAATTTGAT 2 1 0 ATGCCATTAT 0.948982 -61 CTCCCGCTGTTTGCGAGCATTTGCTTTTAACAGCGG 6 22 0 TTGCCATTTT 0.985674 -141 CAGCGGGAGGATACAGCCAATTCTTTTTTTTATGCT 6 49 1 ATACCATTTT 0.977468 -114 TGCATCTAGCTTACATACACTTTATTTCTTCACAGA 8 31 1 TTACCATTTT 0.970859 -157 TCCTCCACCAATGAATACATTTAATTTCGATTCTAG 8 154 0 ATGACATTTT 0.920772 -34 TTTCTCTTACTTGCTCTCATTTTTTTCTGAGACAGG 9 200 1 TTGCCATTTT 0.985675 -101 TCCCAAAAGGATACATTCAGTTCGTTTATTATCATT 9 262 0 ATACCATTTT 0.977468 -39 **** ** ** ** Masking position 9 Map Score: 5.15023 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 33 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 TATAACATATTTTTCAGCAAAAAG 3 4 0 TTTTCAGAAA 0.923989 -66 GCATTAACGCTTTTAAGTAAGACTACTATAA 3 30 0 TTTTAAGAAG 0.89536 -40 ATAGCTTGTTTTATCAGGAAATTGTATTGTT 4 179 0 TTATCAGAAA 0.963818 -58 GATTGATTAATTATCAGAAAGATGTTACGAT 5 44 1 TTATCAGAAG 0.947076 -72 GTCCCCGCTGTTAAAAGCAAATGCTCGCAAA 6 18 1 TTAAAAGAAA 0.880152 -145 ACTTTATTTCTTCACAGAAAAGCCCCTTTCT 8 49 1 TTCACAGAAA 0.847359 -139 AGTGAATGCCCTGTCAGGAAGCCCATGCTCT 8 100 0 CTGTCAGAAG 0.832859 -88 ATATGCCCCGCTAAAAGCAAAGTGAATGCCC 8 120 0 CTAAAAGAAA 0.782141 -68 TTAAACGGCTTTTTAAGAAAAACTGCACTCT 9 164 0 TTTTAAGAAA 0.902007 -137 ******* *** Masking position 6 Map Score: 4.16363 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 279 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 8 GTTGCTTATTTTCACAATGA 4 1 0 TTCACAATGA 0.89035 -236 AGAGGTCTGATGCACACTGCCATTCAACCC 4 100 0 TGCACACTGC 0.978183 -137 TGTATAGGCTTTCACACTGCACACCGAAAT 5 73 0 TTCACACTGC 0.985214 -43 TGACAGGGCATTCACTTTGCTTTTAGCGGG 8 115 1 TTCACTTTGC 0.967015 -73 ACAGAAATTCTTCACTTTGTTGGACAAACA 9 128 1 TTCACTTTGT 0.880651 -173 TAAGAAAAACTGCACTCTGAGGAATGTTTG 9 152 0 TGCACTCTGA 0.973773 -149 TTCTTCACAGTTCAGTCTGATTCTAAACCT 9 233 0 TTCAGTCTGA 0.913848 -68 ********** Masking position 4 Map Score: 5.94606 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 189 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 AAACTCATTCTCTGCTACCCTATTCTCTAA 1 72 0 TCTGCTACCC 0.899782 -144 ACATTATGTTTATTCTACCCAAAAGAAGTC 1 114 1 TATTCTACCC 0.849022 -102 TATAGTATTTTATCCTCTCATGCCATCTTC 1 166 1 TATCCTCTCA 0.775046 -50 ATCTTCTCATTCTCCTTGCCATAAGGAGTG 1 190 1 TCTCCTTGCC 0.799338 -26 AGTTTTCTCATATTCTCCACATTTTCTCTA 2 27 0 TATTCTCCAC 0.835299 -35 GACTTCTTCTCCCTTCATCGCATT 3 56 0 TCTTCTCCCT 0.90689 -14 CTCTACTCTCCCAGTCTCGCT 4 226 0 TCTACTCTCC 0.858311 -11 TTAAGAAATTTCTCCGCCCCGGATTGATTA 5 23 1 TCTCCGCCCC 0.985143 -93 ATTCTCCACCCCATCATTATGT 5 104 0 TCTCCACCCC 0.978137 -12 GAATTGGCTGTATCCTCCCGCTGTTTGCGA 6 42 0 TATCCTCCCG 0.949487 -121 GTTCTATGTCCTCCACCAATGAATAC 8 172 0 TGTCCTCCAC 0.890076 -16 GCCTTTCACCTCCTCCCAAAAGGATACA 9 283 0 CCTCCTCCCA 0.91266 -18 ********** Masking position 3 Map Score: 6.81083 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 549 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 10 AAGAAAGACTTCTTTTGGGTAGAATAAACA 1 120 0 TCTTTTGGGT 0.941696 -96 AAGAAGTCTTTCTTTTGGGTTTATTTGTTA 1 136 1 TCTTTTGGGT 0.941696 -80 TGCTCTCACTCCTTATGGCAAGGAGAATG 1 197 0 TCCTTATGGC 0.833443 -19 CGGTTTTTGTTCTGTTTTGTAAAGGTTTAC 4 55 1 TCTGTTTTGT 0.797137 -182 AGTCTCGCTGTCTTTTTGTCCTAGTATAGC 4 205 0 TCTTTTTGTC 0.942807 -32 TACAGCCAATTCTTTTTTTTATGCTATAAT 6 60 1 TCTTTTTTTT 0.895398 -103 TTCCTTTTTTTCCTTTTTTCATCC 9 5 0 TCCTTTTTTC 0.891588 -296 TTACTTGCTCTCATTTTTTTCTGAGACAGG 9 206 1 TCATTTTTTT 0.678643 -95 ACTGAATGTATCCTTTTGGGAGGAGGTGAA 9 277 1 TCCTTTTGGG 0.922132 -24 ********** Masking position 5 Map Score: 1.61185 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 274 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 TAGGACAAAAAGACAGCGAGACTGGGAGAG 4 212 1 AGACAGCGAG 0.981013 -25 CATTTGCTTTTAACAGCGGGGACAGCCAGC 6 11 0 TAACAGCGGG 0.981316 -152 AAATGCTCGCAAACAGCGGGAGGATACAGC 6 36 1 AAACAGCGGG 0.992521 -127 TAAAGATAGAGGGTGCTATAA 7 4 1 AGATAGAGGG 0.928594 -18 ********** Masking position 5 Map Score: 0.574761 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 154 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 ********** No masking Map Score: 1.43773e-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: 1.43773e-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: 1.43773e-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