AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_hinf_reg_100.orf -o00720_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0024 37 citrate lyase, gamma chain (citD) #2 HI0025 250 citrate lyase ligase (citC) #3 HI0835 181 fumarate reductase, flavoprotein subunit (frdA) #4 HI1194 300 glycine cleavage system transcriptional activator (gcvA) #5 HI1196 35 succinyl-CoA synthetase, beta subunit (sucC) #6 HI1210 206 malate dehydrogenase (mdh) #7 HI1636 182 phosphoenolpyruvate carboxylase (ppc) Motif number 1 GCAAGCAAAAAGTGCGGTTTAATTTAGCGGAATT 2 16 0 AGTGGTTATT 0.991359 -235 TTGCAACAAAAGTGCGGTTTATTTTTACAACTCA 2 46 1 AGTGGTTATT 0.991359 -205 CTAACTTGGTAGTGATGTTATGTTTTCTTCTTTT 2 216 1 AGTGGTTTTT 0.996069 -35 TTACCCTTTTAGGGGATTTATTTTTACTTTCTAT 3 143 1 AGGGTTTTTT 0.901331 -39 GCTCTCATTGAGTGGCGTTTTTTTCATCCCGATT 4 14 0 AGTGGTTTTT 0.996069 -287 CCAATCATTAAGTATGGTTGTATTGTAAGGAAAA 4 184 1 AGTAGTTTTT 0.956778 -117 GGAAAGGACAAGTGACGTTTTTTTATTTGAGGTA 4 223 1 AGTGGTTTTT 0.996069 -78 AGTTGATGAAAGTGAATTTTTATGCAATTCTTAT 6 38 0 AGTGTTTTTG 0.901331 -169 TTTTTTAAAAAGTGCGGTCTATTTTTGCTAAGT 7 10 0 AGTGGTCATT 0.959884 -173 ATCCCTAAAAAGTGCGGGTCTTTTTTAGCTATTT 7 43 1 AGTGGGTTTT 0.981427 -140 **** *** * ** Masking position 13 Map Score: 18.4214 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 216 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 2 CTAAATTAAACCGCACTTTTTGCTTGCAAC 2 23 1 CCGCACTTTT 0.996982 -228 TAAAAATAAACCGCACTTTTGTTGCAAGCA 2 43 0 CCGCACTTTT 0.996982 -208 TCATATTTTTCCCAACTTTATAATCTAATA 2 137 0 CCCAACTTTA 0.959373 -114 GTTCGGGAAACCGAACTTGAGTAACAATTT 4 97 0 CCGAACTTGA 0.974224 -204 GTTCGGTTTCCCGAACTATATGCAAACACA 4 111 1 CCGAACTATA 0.962266 -190 CAAAAATAGACCGCACTTTTTAAAAAATCC 7 17 1 CCGCACTTTT 0.996982 -166 TAAAAAAGACCCGCACTTTTTAGGGATTTT 7 40 0 CCGCACTTTT 0.996982 -143 ********** Masking position 5 Map Score: 16.1218 Number of sites scoring better than the average of aligned sites = 1285 Number in coding regions = 832 Number in noncoding regions = 453 Number of orfs with sites within 600 bp upstream = 297 Fraction of orfs with sites within 600 bp upstream = 0.0477032 Motif number 3 GGTTTAATTTAGCGGAATTTTAAA 2 4 0 AGGGAATTTT 0.939929 -247 CTAACTTGGTAGTGATGTTATGTTTTCTTCT 2 216 1 AGGATGTTAT 0.912071 -35 TTACCCTTTTAGGGGATTTATTTTTACTTTC 3 143 1 AGGGATTTAT 0.902206 -39 GCTCTCATTGAGTGGCGTTTTTTTCATCCCG 4 17 0 AGGGCGTTTT 0.966918 -284 GGAAAGGACAAGTGACGTTTTTTTATTTGAG 4 223 1 AGGACGTTTT 0.972553 -78 AGTTGATGAAAGTGAATTTTTATGCAATTCT 6 41 0 AGGAATTTTT 0.972522 -166 CGCACTTTTTAGGGATTTTTTAAAAAGTGCG 7 28 0 AGGATTTTTT 0.964515 -155 GGTCTTTTTTAGCTATTTTTTAGCTTTTCTT 7 59 1 AGTATTTTTT 0.727131 -124 AATGCTATTCAGAGAAATTTTGAAAATAATC 7 90 0 AGGAAATTTT 0.949924 -93 ** ******** Masking position 8 Map Score: 8.18404 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 189 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 AACTCAGAATAACCGCCAATATTGCCTATAAATTATTCAATGTA 2 74 1 AAGAATTTAT 0.979177 -177 TCCCAACTTTATAATCTAATATTATCTTCACACTGCATTATACA 2 114 0 ATTAATTTAT 0.967752 -137 TGGGAAAAATATGAGCTTATCTTGTATCGTAATTTGCTCATCGC 2 153 1 ATGTATTTAT 0.87891 -98 TCTACCTCAAAAAAGCTAAGATTGAGTTGAGAGTAGCTCTCGTT 3 15 0 AAGAATTTAT 0.979617 -167 AAATCCCCTAAAAGGGTAATATTGTGTGGGCATTGTGCCATTTT 3 118 0 AAGAATTTAT 0.979617 -64 TTTCGTCTATAATGGACAAGATTTATTTCAAATTAGTTTTTCTA 4 258 0 AAGAATTTAT 0.906414 -43 TTATTTTTCAATAGTCAAAATTTGCATAAGAATTGCATAAAAAT 6 13 1 ATTAATTTAT 0.967774 -194 TGTGAACTAGATCATAGAATGATATTTCTCTATTTGTAATTGTA 6 117 1 ATTAAATTAT 0.69615 -90 AAACAGACTGATTTTAAAATGTTCATCTTACAATTACAAATAGA 6 145 0 ATTAATTCAT 0.847107 -62 TTTTTTAGCTATTTTTTAGCTTTTCTTGATTATTTTCAAAATTT 7 63 1 ATTAGTTTAT 0.845443 -120 ATCTATCGCCAACTGACAAATTTTATTTTTTACTTTTAGGAGTT 7 146 1 AAGAATTTAT 0.979614 -37 ** * ** ** * * * Masking position 22 Map Score: 9.18322 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 102 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TTGAATAATTTATAGGCAATATTGGCGGTTATTC 2 80 0 TTAGAAATTG 0.829324 -171 TAATGCAGTGTGAAGATAATATTAGATTATAAAG 2 118 1 TAAGAAATTA 0.702206 -133 ACGATACAAGATAAGCTCATATTTTTCCCAACTT 2 149 0 AAAGCAATTT 0.909049 -102 TCTACCTCAAAAAAGCTAAGATTGAGTTGAGAGT 3 25 0 AAAGAAATTG 0.947543 -157 AAATCCCCTAAAAGGGTAATATTGTGTGGGCATT 3 128 0 AAGGAAATTG 0.936943 -54 TTTCGTCTATAATGGACAAGATTTATTTCAAATT 4 268 0 ATGGAAATTT 0.924843 -33 CTTGTCCATTATAGACGAAAATTTTATAA 4 282 1 AAGAAAATTT 0.83968 -19 TTTATTTTTCAATAGTCAAAATTTGCATAAGAAT 6 12 1 ATAGAAATTT 0.937336 -195 AAGAACAAAGAGAAGAAAATATTTATCTCAGAAA 6 83 1 AAAGAAATTT 0.966488 -124 CATTCTATGATCTAGTTCACATTTCTGAGATAAA 6 104 0 TTAGCAATTT 0.728903 -103 TTTGTAATTGTAAGATGAACATTTTAAAATCAGT 6 149 1 TAGAAAATTT 0.729849 -58 TCCTAAAAGTAAAAAATAAAATTTGTCAGTTGGC 7 153 0 AAAAAAATTT 0.86424 -30 * *** ** **** Masking position 9 Map Score: 8.17289 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 378 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 6 ACAACTCAGAATAACCGCCAATATTGCCTATA 2 72 1 ATACCCCAAT 0.911881 -179 TAATTTGCTCATCGCTTATAATAGCTCTATAC 2 182 1 ATCCTATAAT 0.745824 -69 AAAACATAACATCACTACCAAGTTAGTAGTAT 2 210 0 ATCCTCCAAG 0.920912 -41 GTAAAAATAAATCCCCTAAAAGGGTAATATTG 3 138 0 ATCCCAAAAG 0.980262 -44 GATATCCTCCAATCAATAGAAAG 3 169 0 ATACCCCAAT 0.911884 -13 CTTGTCCATTATAGACGAAAATTTTATAA 4 282 1 ATAACAAAAT 0.646446 -19 AACTGTTTTCATAACCAAAAAGGACGTCGCGA 5 14 1 ATACCAAAAG 0.973689 -22 TTTTTAAAAAATCCCTAAAAAGTGCGGGTCTT 7 33 1 ATCCTAAAAG 0.963115 -150 AAGCTAAAAAATAGCTAAAAAAGACCCGCACT 7 53 0 ATACTAAAAA 0.750629 -130 GGCGATAGATATAACTAAAAATAGGGTGGAGG 7 124 0 ATACTAAAAT 0.924247 -59 AGGAACTCCTAAAAGTAAAAAATAA 7 168 0 AACCCAAAAG 0.863206 -15 *** ** ***** Masking position 10 Map Score: 6.03104 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 231 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 7 AGATTTTCCTTCCGTATATTGAT 1 25 0 TTTTCCTTCC 0.986445 -13 AAGCTCATATTTTTCCCAACTTTATAATCT 2 141 0 TTTTCCCAAC 0.860792 -110 ATTGTGCCATTTTTCGTTACAAATTAATAA 3 101 0 TTTTCGTTAC 0.903429 -81 GGGGATTTATTTTTACTTTCTATTGATTGG 3 154 1 TTTTACTTTC 0.706798 -28 AGTGGCGTTTTTTTCATCCCGATTTTA 4 8 0 TTTTCATCCC 0.815129 -293 TTTGTTACTCATTTACTTCCTGTATATTAT 4 70 0 ATTTACTTCC 0.799008 -231 AATGATTGGTAATTCCTTACTAGTTAATGA 4 163 0 AATTCCTTAC 0.715368 -138 TTTCCTACCCTTTTCCTTACAATACAACCA 4 198 0 TTTTCCTTAC 0.982616 -103 GTCACTTGTCCTTTCCTACCCTTTTCCTTA 4 209 0 CTTTCCTACC 0.910225 -92 GTGAACTGTTTTCATAACCAAAAAGGAC 5 9 1 TTTTCATAAC 0.85377 -27 ********** Masking position 4 Map Score: 5.19235 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 156 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 CCGTATATTGATGAATAAAAATGTAT 1 6 0 ATGAATAAAA 0.97558 -32 TAAAATCGGGATGAAAAAAACGCCACTCAAT 4 11 1 ATGAAAAAAC 0.795269 -290 CAGGAAGTAAATGAGTAACAAATTGTTACTC 4 78 1 ATGAGTAAAA 0.957665 -223 GAAACCGAACTTGAGTAACAATTTGTTACTC 4 90 0 TTGAGTAAAA 0.95762 -211 ATTTTGACTATTGAAAAATAAAG 6 3 0 TTGAAAAAAA 0.935997 -204 TAGTCAAAATTTGCATAAGAATTGCATAAAA 6 24 1 TTGCATAAAA 0.957666 -183 TGCATAAGAATTGCATAAAAATTCACTTTCA 6 35 1 TTGCATAAAA 0.957666 -172 CAACTGAAATATGAATAAGAACAAAGAGAAG 6 67 1 ATGAATAAAA 0.97558 -140 ******** ** Masking position 7 Map Score: 8.33798 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 61 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 GGAAAAATATGAGCTTATCTTGTATCGTAA 2 155 1 GAGCTTATCT 0.942862 -96 TGTAAACGAGAGCTACTCTCAACTCAATC 3 10 1 GAGCTACTCT 0.929119 -172 AACTCAATCTTAGCTTTTTTGAGGTAGATC 3 31 1 TAGCTTTTTT 0.956762 -151 TATTTCAAATTAGTTTTTCTAATACCTCAA 4 249 0 TAGTTTTTCT 0.91016 -52 GGGTCTTTTTTAGCTATTTTTTAGCTTTTC 7 58 1 TAGCTATTTT 0.922238 -125 AGCTATTTTTTAGCTTTTCTTGATTATTTT 7 69 1 TAGCTTTTCT 0.984959 -114 ********** Masking position 5 Map Score: 3.04791 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 31 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ********** No masking Map Score: -1.39734e-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: -1.39734e-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: -1.39734e-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