AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_mthe_reg_300.orf -o00300_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH413 300 conserved protein #2 MTH415 199 conserved protein #3 MTH531 291 UDP-N-acetylmuramyl tripeptide synthetase related protein #4 MTH532 28 UDP-N-acetylmuramyl tripeptide synthetase related protein #5 MTH533 41 unknown #6 MTH800 52 dihydrodipicolinate reductase #7 MTH802 49 aspartokinase II alpha subunit #8 MTH804 40 chorismate mutase, subunit A #9 MTH805 240 conserved protein (homoserine kinase related) #10 MTH1231 40 conserved protein #11 MTH1232 25 homoserine dehydrogenase #12 MTH1335 73 diaminopimelate decarboxylase #13 MTH1542 37 conserved protein #14 MTH1543 229 thiamine biosynthesis protein #15 MTH1544 219 ribokinase #16 MTH1545 63 conserved protein Motif number 1 GAACCCTTAAATTTGTGTTCAGAGGGCTGTGGTTCCTTGATG 1 43 0 ATTTCGGTGG 0.963834 -258 TGATTCTGTGATGAGGCCCCTGTGGGTTCTGGAGGTCTTTAT 1 94 0 ATCCCGGTGG 0.987604 -207 AAGACAGCGAATTCAAACCCTCTGCATACAGATATGCGCCTG 1 181 0 ATCCCCCAGA 0.823412 -120 GGTTAAATTTATTACCCCTCCCCGGTAATAGATAAACGGTGA 1 263 1 ATCTCCGAGA 0.953926 -38 CACAGGATCCATGTTCCCTCTGCTGAATCTGAGGCCATGTTT 2 38 1 ATCTCGGTGA 0.94059 -162 CATAAAGTCTATGGTGCTGCAGTGATATAAGGCTTAGTCTAT 2 130 0 ATTGCGAAGG 0.742701 -70 TCAGTAATCCATGAACTCCCTGGAGTGTTAGAGGTGAT 3 7 0 ATCCCGGAGA 0.984871 -285 CTATGGGTGGATACATATCCTCCCGGGTGAGGATCTTTAGGT 3 115 1 ATTCCCGAGG 0.986632 -177 GAGTCACCTGATGGCACCCGTCCTGACCGAGGTAGTGGGTGT 3 198 0 ATCCGCGAGG 0.897307 -94 GAGGCTCATGATGGTCCTGGAGGAACTGGCACTGATCTA 6 8 1 ATTCCGGTGG 0.982589 -45 AATATATTAATCTTCTCTAAAAAAAGGAGTGGGTGGT 13 11 0 ATTTCCAAGG 0.863363 -27 ATATCCATATATCTCATTTCCGCTGATCCAGATCATACCCTC 14 165 1 ATTTCGGAGA 0.956093 -65 GCCTCAAAGTATAAAGTCCCACCCAATAAAGGATGCTCAACA 15 98 1 ATCCCCAAGG 0.949723 -122 AAGGGCCTGGAATATGGTCCGGTTGATTATGAAACCCTGAAA 16 15 1 AATCCGGTGA 0.684958 -49 CTATGGTGTTTCTGTGGTTTCAGGGTTTCATAAT 16 40 0 ATTTCGGAGG 0.981041 -24 ** *** * * *** Masking position 1 Map Score: 15.5201 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 607 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 2 CCTTAAATTTGTGTTCAGAGGGCTGTGGTTCCTTGAT 1 44 0 GTTCGGGTTG 0.985182 -257 TCTGTGATGAGGCCCCTGTGGGTTCTGGAGGTCTTTA 1 95 0 GCCCGGGTTG 0.982375 -206 GGATCCATGTTCCCTCTGCTGAATCTGAGGCCATGTT 2 42 1 TCTCGGATTG 0.943478 -158 CTAAAGATCCTCACCCGGGAGGATATGTATCCACCCA 3 118 0 TCCCGGGTTG 0.991024 -174 TACCTATGGATCATTCGGTGGGATATCTACCAGAGGC 3 162 0 TTTCGGGTTC 0.962653 -130 AGGCTCATGATGGTCCTGGAGGAACTGGCACTGATCT 6 12 1 TTCCGGGATG 0.939558 -41 CTCCAGTCATGTTTTCAGGAGTTTTTGTTATATCAGA 9 29 1 GTTCGGTTTG 0.911056 -212 AATGACAATATAAGTCCTTAGGGTGTGAAGAT 12 6 0 TGTCTGGTTG 0.795636 -68 GTTTGACCCTTAACCCGTGAGGGTATGATCTGGATCA 14 188 0 TCCCTGGTTG 0.933195 -42 CCATAAATGGTTTTTCAGCGGGTTTTCATGC 15 5 0 TTTCGGGTTC 0.962653 -215 AATATGGGGTTAATTCTGTTGGGGTTGGTTTATAATG 15 179 0 TTTCGGGGTG 0.957643 -41 GCCTGGAATATGGTCCGGTTGATTATGAAACCCTGAA 16 19 1 TTCCGGATTG 0.953866 -45 CTATGGTGTTTCTGTGGTTTCAGGGTTTCATAA 16 41 0 TTTCGGTTAG 0.683469 -23 * *** * ** * ** Masking position 6 Map Score: 13.6792 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 402 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 ATCCATCAAGGAACCACAGCCCTCTGAACACA 1 40 1 GACCACGCCC 0.984105 -261 CATGATTCTGTGATGAGGCCCCTGTGGGTTCT 1 106 0 TATGAGCCCC 0.862391 -195 GTTTTCGACAGGATCCCGGCCCAGGTTTTTAC 1 150 1 GATCCCGCCC 0.97383 -151 GTTCATGCAGGGATCACCCCCCTTGATTCCGG 1 232 1 GATCACCCCC 0.995948 -69 GTTAAATTTATTACCCCTCCCCGGTAATAGAT 1 264 1 TACCCCCCCC 0.936777 -37 TCCTATATAGCTATCAGATCCCGGGTCAGGCA 3 55 0 CATCAGTCCC 0.902953 -237 GCATCACACCCCCTAGATCAGT 6 41 0 GATCACCCCC 0.995948 -12 AAAAACTACTGTTTCAGTCCCCGTTAATACTC 14 107 0 GTTCAGCCCC 0.971897 -123 ACCATTTATGGGATCAGTTCCCTGCATGAAAT 15 31 1 GATCAGTCCC 0.982522 -189 ATGCTCAACAGAACCAGGCCCAATCCATCTAT 15 130 1 GACCAGCCCA 0.938609 -90 * ***** **** Masking position 10 Map Score: 11.8769 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 245 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 AATTCAGAGTATCCATCAAGGAACCACAGCCCTCTGAA 1 30 1 ATCCAACCAA 0.989949 -271 AGGTCTTTATATCCCCTGAGAACCCTTAAATTTGTGTT 1 66 0 ATCCCACCTA 0.979551 -235 AAGGGGGGTGATCCCTGCATGAACCTGAGGAGAAAGAC 1 218 0 ATCCCACCTA 0.979551 -83 TATATCAGACATCCATGTACCATCCTAAATTTTTAACC 9 57 1 ATCCAACCTA 0.985354 -184 CTAAAGTTTAATCAAATCTTTATCCAAATGACAATATA 12 31 0 ATCAAACCAA 0.965268 -43 GATGGAACCAATCAATATGATATCCATATATCTCATTT 14 146 1 ATCAAACCAA 0.965268 -84 ATTTCCGCTGATCCAGATCATACCCTCACGGGTTAAGG 14 180 1 ATCCAACCTA 0.985354 -50 TGCTCAACAGAACCAGGCCCAATCCATCTATAACGAAT 15 131 1 AACCAACCAC 0.921709 -89 GAATAATCCAATCACATTATAAACCAACCCCAACAGAA 15 165 1 ATCACACCAC 0.894829 -55 GAAACCCTGAAACCACAGAAACACCATAG 16 45 1 AACCACCCAA 0.850969 -19 ***** * *** * Masking position 1 Map Score: 11.2992 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 73 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 CTCTGAACACAAATTTAAGGGTTCTCAGGG 1 61 1 AAATTTAAGG 0.816373 -240 ATCCCTGCATGAACCTGAGGAGAAAGACAG 1 216 0 GAACCTGAGG 0.973926 -85 TCCCTCTGCTGAATCTGAGGCCATGTTTTT 2 52 1 GAATCTGAGG 0.947603 -148 CCCGGGTGAGGATCTTTAGGTAGACTGCCT 3 136 1 GATCTTTAGG 0.84259 -156 TTATTTATATAAAATTGAGGT 5 31 1 AAAATTGAGG 0.952507 -11 AAAATGGTTAAAAATTTAGGATGGTACATG 9 70 0 AAAATTTAGG 0.886872 -171 CAGTGTTTGAGAGCTTGAGGTGCTCTCTGG 9 170 1 GAGCTTGAGG 0.953043 -71 AGATTTGATTAAACTTTAGGGAGGATCAAC 12 50 1 AAACTTTAGG 0.958679 -24 TCCCTGCATGAAATTTGAGGACCACATTTT 15 49 1 AAATTTGAGG 0.966373 -171 ********** Masking position 6 Map Score: 6.86434 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 418 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 GCCTTCAATCCATGATTCTGTGATGAGGCCCCTG 1 114 0 CATGTTTTAT 0.770397 -187 TCTCTGTGGCAAGGTTTATATCATTGTAGCACGA 2 97 1 AAGGTTTTAT 0.955481 -103 CGGGTGCCATCAGGTGACTCTTATTCACAGATTA 3 220 1 CAGGGATTAT 0.973201 -72 ATCAGGAAGGAACGCGTGTTTAATAAAAACGTTT 3 254 1 AACGGTTTAT 0.879625 -38 GAATGGAAGAAAGGGGAATGTAATTT 8 25 1 AAGGGATTAT 0.957934 -16 GTCATGTTTTCAGGAGTTTTTGTTATATCAGACA 9 34 1 CAGGGTTTTT 0.9186 -207 TCCAGGATTCTATGATCGTTCACTGA 9 225 0 CAGGTTTTAT 0.971612 -16 TAATACTCTTAAGGAGTCTTTGATGTCTCCCCTA 14 81 0 AAGGGTTTAT 0.980504 -149 GAGGCGGATTAAGGTGATTTTTATAAAATGTGGT 15 69 0 AAGGGATTAT 0.957934 -151 TCTGTGGTTTCAGGGTTTCATAATCAACCGGACC 16 30 0 CAGGTTCTAT 0.877116 -34 **** ** * * ** Masking position 11 Map Score: 8.72132 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 86 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 TTCAAACCCTCTGCATACAGATATGCGCCT 1 182 0 CTGCATACAG 0.717982 -119 CCTCAGGTTCATGCAGGGATCACCCCCCTT 1 226 1 ATGCAGGGAT 0.821873 -75 AGGATGACCACTGCAGACATGGG 2 4 0 CTGCAGACAT 0.961603 -196 GTCTATGGTGCTGCAGTGATATAAGGCTTA 2 136 0 CTGCAGTGAT 0.975915 -64 ACCTCTAACACTCCAGGGAGTTCATGGATT 3 14 1 CTCCAGGGAG 0.830572 -278 CTCCAGTGACCCTTGAATGG 8 1 1 CTCCAGTGAC 0.948658 -40 ACCTTTTTACCTCCAGTCATGTTTTCAGGA 9 19 1 CTCCAGTCAT 0.961389 -222 CTGCAAAGCACTCCAGAGAGCACCTCAAGC 9 182 0 CTCCAGAGAG 0.975236 -59 ********** Masking position 5 Map Score: 5.89012 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 335 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 ATCCCGGCCCAGGTTTTTACAGGCGCATATCTGTATG 1 162 1 ATTTACGGCA 0.942208 -139 CCGGGATCTGATAGCTATATAGGATGAGAACATATCT 3 63 1 ATATATGGGA 0.970613 -229 GGATGAGAACATATCTTTATAGGTAGAGTGTCTATGG 3 84 1 ATTTATGGGA 0.981476 -208 TGTTTAATAAAAACGTTTATGGGTGCATTTAA 3 270 1 ATTTATGGCA 0.981476 -22 GTAAGATATATATTGTATGATTATTTATAT 5 4 1 ATATATGTGA 0.883101 -38 TAAGTGCAATATTTATATAGTGGTAGAACATTCTATT 9 104 0 ATATAGGGGA 0.910416 -137 ATGAAAAGATTTATAGTCACATCAGGCATTT 10 5 1 ATTTATGTCA 0.923774 -36 CCCGCTGAAAAACCATTTATGGGATCAGTTCCCTGCA 15 20 1 ATTTATGGCA 0.981476 -200 * ***** ** ** Masking position 9 Map Score: 3.43067 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 11 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GCCTCATCACAGAATCATGGATTGAAGGCC 1 119 1 AGAATCATGG 0.935688 -182 ATGCGCCTGTAAAAACCTGGGCCGGGATCC 1 160 0 AAAAACCTGG 0.960241 -141 CACAGAGAGAAAAAACATGGCCTCAGATTC 2 62 0 AAAAACATGG 0.966975 -138 CTACAATGATATAAACCTTGCCACAGAGAC 2 96 0 ATAAACCTTG 0.826262 -104 CATTCTATTAATAAAAATGGTTAAAAATTT 9 83 0 ATAAAAATGG 0.81916 -158 CTACCACTATATAAATATTGCACTTAGATA 9 115 1 ATAAATATTG 0.692661 -126 GAACGATCATAGAATCCTGGA 9 230 1 AGAATCCTGG 0.923082 -11 AGCGGAAATGAGATATATGGATATCATATT 14 159 0 AGATATATGG 0.739383 -71 TGATCACCTGAAAAATATGGGGTTAATTCT 15 199 0 AAAAATATGG 0.919648 -21 ********** Masking position 3 Map Score: 2.88313 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 179 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 GACAGCGAATTCAAACCCTCTGCATACAGA 1 191 0 TCAAACCCTC 0.991131 -110 ATCACCTCTAACACTCCAGGGAGTTC 3 7 1 TCTAACACTC 0.886727 -285 GCATCACACCCCCTAGATCAGTG 6 40 0 TCACACCCCC 0.952321 -13 CCTCAAGCTCTCAAACACTGCAAAGTGTAT 9 160 0 TCAAACACTG 0.94854 -81 ATCTTCACACCCTAAGGACTTATA 12 5 1 TCACACCCTA 0.920846 -69 AGGGGAGACATCAAAGACTCCTTAAGAGTA 14 82 1 TCAAAGACTC 0.878491 -148 CTGATCCAGATCATACCCTCACGGGTTAAG 14 187 1 TCATACCCTC 0.964998 -43 CGGTTGATTATGAAACCCTGAAACCACAGA 16 34 1 TGAAACCCTG 0.886423 -30 ********** Masking position 5 Map Score: 5.48557 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 125 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 GTCGAAAACTGGCCTTCAATCCATGATTCTG 1 128 0 GCCTTCAATC 0.721176 -173 ATTATATCACCGTTTATCTATTACCGGG 1 283 0 CCCGTTTATC 0.768568 -18 TCCACCCATAGACACTCTACCTATAAAGATA 3 95 0 GCACTCTACC 0.953691 -197 ATCTACCAGAGGCAGTCTACCTAAAGATCCT 3 144 0 GCAGTCTACC 0.925527 -148 TCCATAGGTACACCCACTACCTCGGTCAGGA 3 189 1 CCCCACTACC 0.894717 -103 TGATTCACCGTTAACTGCTCTTTAAG 4 13 0 CCCGTTAACT 0.729401 -16 GCAAGCCGTGGCCCCTCAACTAGGGGAGACA 14 61 1 GCCCTCAACT 0.943564 -169 CTTCTGGTTTGACCCTTAACCCGTGAGGGTA 14 200 0 GCCCTTAACC 0.977384 -30 CCATATTCCAGGCCCTTTACC 16 1 0 GCCCTTTACC 0.981564 -63 * ********* Masking position 9 Map Score: 2.50819 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 580 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 ACATGGATCCTGTGTGACAGGATGACCACTG 2 21 0 TGTGTGCAGG 0.99062 -179 GTTTTTTCTCTCTGTGACAGGTCTCTGTGGC 2 76 1 TCTGTGCAGG 0.982259 -124 GTGACAGGTCTCTGTGGCAAGGTTTATATCA 2 89 1 TCTGTGCAAG 0.954841 -111 ACCCCCTAGATCAGTGCCAGTTCCTCCAGGA 6 25 0 TCAGTGCAGT 0.838467 -28 TGCTACGCATTGTGTATCATGTTTGTCAGAG 14 26 0 TGTGTACATG 0.877281 -204 TGATACACAATGCGTAGCAGGCAGCAAGCCG 14 38 1 TGCGTACAGG 0.943838 -192 ****** **** Masking position 5 Map Score: 1.1018 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 78 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 ATGCAGGGATCACCCCCCTTGATTCCGGGTT 1 236 1 CACCCCCTTG 0.770647 -65 CACCTGATGGCACCCGTCCTGACCGAGGTAG 3 205 0 CACCCTCCTG 0.949925 -87 TTAAACACGCGTTCCTTCCTGATTAATCTGT 3 246 0 GTTCCTCCTG 0.971268 -46 AGACATCCATGTACCATCCTAAATTTTTAAC 9 63 1 GTACCTCCTA 0.839476 -178 TAGTGTTGATCCTCCCTAAAGTTTAATC 12 56 0 GATCCCCCTA 0.941507 -18 TGGGGCCCCCCCAGACTCTGACAA 14 4 1 GGCCCCCCAG 0.968845 -226 ATATTGATTGGTTCCATCCAGTTATAAAAAC 14 133 0 GTTCCTCCAG 0.954694 -97 AAAGTATAAAGTCCCACCCAATAAAGGATGC 15 103 1 GTCCCCCCAA 0.964265 -117 ***** ***** Masking position 5 Map Score: 1.73293 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 600 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 ********** No masking Map Score: -2.27841e-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 15 ********** No masking Map Score: -2.27841e-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