AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_mthe_reg_100.orf -o00260_mthe_100.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 MTH248 195 conserved protein #2 MTH249 64 conserved protein #3 MTH250 23 tRNA intron endonuclease #4 MTH251 54 tryptophanyl-tRNA synthetase #5 MTH252 22 conserved protein #6 MTH253 75 threonine synthase #7 MTH415 199 conserved protein #8 MTH800 52 dihydrodipicolinate reductase #9 MTH802 49 aspartokinase II alpha subunit #10 MTH804 40 chorismate mutase, subunit A #11 MTH805 240 conserved protein (homoserine kinase related) #12 MTH970 77 phosphoglycerate dehydrogenase #13 MTH1026 222 phosphatidylserine decarboxylase #14 MTH1027 39 CDP-diacylglycerol-serine O-phosphatidyltransferase #15 MTH1120 132 nifH / minD related protein #16 MTH1122 39 seryl-tRNA synthetase #17 MTH1231 40 conserved protein #18 MTH1232 25 homoserine dehydrogenase #19 MTH1380 167 serine hydroxymethyltransferase #20 MTH1455 192 threonyl-tRNA synthetase #21 MTH1627 220 TATA-binding transcription initiation factor #22 MTH1648 110 dihydrolipoamide dehydrogenase #23 MTH1850 105 fumarate reductase Motif number 1 ACCCGGGGCCCCTCAAGGTATAATATTCCT 1 39 0 CCTCAAGGTA 0.925417 -157 ACACGGAAGGCCTCCCGGGCATCACGGGAC 1 67 0 CCTCCCGGGC 0.990356 -129 AACCAGCACCCCTCCAGCGGAATATTCCCC 1 101 0 CCTCCAGCGG 0.98409 -95 CAGGGGAAATCCTTCAGGGCGCTGACACCC 1 150 0 CCTTCAGGGC 0.958768 -46 AAACCCTGACCCTCCAGGGGAAATCCTTCA 1 164 0 CCTCCAGGGG 0.992545 -32 ACCTCCCGTGAGTGCTGGTTG 3 13 0 CCTCCCGTGA 0.963973 -11 AGTGCCAGTTCCTCCAGGACCATCATGAGC 8 14 0 CCTCCAGGAC 0.953538 -39 GACCTTTTTACCTCCAGTCATGTTTTCAGG 11 18 1 CCTCCAGTCA 0.887914 -223 CCAGAGAGCACCTCAAGCTCTCAAACACTG 11 170 0 CCTCAAGCTC 0.856408 -71 AAATAATCCTCCTGTGATCCTGTGAGA 15 8 1 CCTCCTGTGA 0.870706 -125 ATTCGGAATCCCCCCAGCTATCAACACGCG 19 74 1 CCCCCAGCTA 0.813476 -94 AGATGATGACCCTTAAGGGATCTCCTGAAC 20 78 0 CCTTAAGGGA 0.810354 -115 CTAGATACCTCCCGGTGAAGTTAAACC 21 204 0 CCTCCCGGTG 0.966369 -17 ********** Masking position 2 Map Score: 16.7532 Number of sites scoring better than the average of aligned sites = 1142 Number in coding regions = 1097 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 GGGGTGCTGGTTTTCCAGGGAACTCTATCTG 1 119 1 TTTCCAGGGA 0.924711 -77 CCCTGAAGGATTTCCCCTGGAGGGTCAGGGT 1 161 1 TTCCCCTGGA 0.969294 -35 GTTAAAGGGGTCTTCCATGGATGACTGCAGC 2 13 0 TTTCCATGGA 0.829951 -52 TCATATCACCGTTATTAAGTCATT 4 41 0 TTCACCGTTA 0.875804 -14 GAAACTTTATTCTTACCGGTAAA 6 63 1 TTTACCGGTA 0.935853 -13 CACAGAGACCTGTCACAGAGAGAAAAAACAT 7 74 0 TTCACAGAGA 0.86959 -126 ACTTTATGTGTTTCACATGTATCCATCAAGT 7 164 1 TTCACATGTA 0.915601 -36 TATATATATCTTTCACCGGCATATCACATTC 13 65 1 TTCACCGGCA 0.958096 -158 GACATGAACATTTCACATGGAGTTCACAGCG 13 122 0 TTCACATGGA 0.971127 -101 GAAATGTTCATGTCACCGTGAACTCCATGTG 13 139 1 TTCACCGTGA 0.956262 -84 ATAGGTTTCTTCTCACATGGAGTTCACGGTG 13 152 0 TTCACATGGA 0.971127 -71 TATCAGATCATATTACCGGTAATGGGAACAG 13 180 1 TTTACCGGTA 0.935853 -43 GTAGGTTTAACTTCACCGGGAGGTATCTAG 21 201 1 CTCACCGGGA 0.961269 -20 * ********* Masking position 11 Map Score: 15.1139 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 420 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 ATAATATTCCTCAGGAACTCAACACTCTGTCTGACCTCA 1 7 0 TCATAAATTG 0.978287 -189 TTTCATTTTTTCCAACATTTAAAAGGTTGTGAAGGTTA 9 22 1 TCATAAATTA 0.955107 -28 GGTAGAACATTCTATTAATAAAAATGGTTAAAAATTTAGGATG 11 77 0 TCATAAATAA 0.923866 -164 AATAGAATGTTCTACCACTATATAAATATTGCACTTAGATACT 11 104 1 TCATTAAATA 0.645675 -137 CAAAGTGTATTCATCAATTAAATAGTATCTAAGTGCAATATTT 11 127 0 TCATAAATTG 0.978287 -114 GATTCTATGATCGTTCACTGAATAGATTATTAGGCTGCAAAGC 11 203 0 TCATAAATTG 0.978287 -38 TATAGATTCTTCTATCATTCTATAAAATCTTCATTGTGATAAG 12 33 1 TCATTAATTA 0.861622 -45 ATATATATACTCATGTACTGAAGATTAAATGTAATCCAAGTTA 13 31 0 TCATAAAATA 0.861623 -192 TATCTCGGTAACCATTAATAAATATTGTCTTGGACAGCAAAGA 15 54 1 ACATAAATTG 0.894234 -79 ATGGAAGTTAACACCAATTTTATATTGTCATTGCAACTATTTT 19 131 1 ACATTAATAG 0.585283 -37 GCACAGAATGTACCTCATTGAAGAGGTTCAGGAGATCCCTTAA 20 53 1 TAATAAATAA 0.584957 -140 GCACCATCCTTAAATAATTTAACATACTTAATGAATAGAGGGG 21 17 0 TAATAAATAG 0.749037 -204 CGTTTATCATTCCTCAATTGAAAAATTATTGCGGCCTATCATC 21 80 0 TCATAAAATG 0.929508 -141 TCAATAACCCTCTCCAAATTAATAGGATTAAAGTCAGAATACA 22 11 1 TCATAAATAG 0.962544 -100 ** * * ** * * * * Masking position 12 Map Score: 10.1724 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 37 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 4 ATGACTTAATAACGGTGATATGA 4 42 1 AAGGTGAAGA 0.937492 -13 AACATGGATCCTGTGTGACAGGATGACCACTGC 7 20 0 CTTGTGAAGA 0.964686 -180 TGTTTTTTCTCTCTGTGACAGGTCTCTGTGGCA 7 75 1 CTTGTGAAGT 0.925073 -125 ATGTATCCATCAAGTTGAGAGGAGTCTGAT 7 180 1 CAGTTGAAGA 0.855821 -20 ATAAAATCTTCATTGTGATAAGTGTGGTGAAAT 12 54 1 CATGTGAAGT 0.971234 -24 GCTGTGAACTCCATGTGAAATGTTCATGTCACC 13 123 1 CCTGTGAAGT 0.949355 -100 ACATGGAGTTCACGGTGACATGAACATTTCACA 13 136 0 CAGGTGAAGA 0.981534 -87 ACCGTGAACTCCATGTGAGAAGAAACCTATCAG 13 153 1 CCTGTGAAGA 0.976869 -70 CTGTGAGAATAACTATGAAATGAGTATCTCGGT 15 30 1 AATATGAAGA 0.805731 -103 ATGGTGCTTAAAATATGAAAAGAGTTTGATGAT 21 53 1 AATATGAAGA 0.805731 -168 ** ***** * ** Masking position 6 Map Score: 7.96283 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 61 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 CGGGGCCCCTCAAGGTATAATATTCCTCAGGAACTCAA 1 28 0 CAGTATCCTC 0.987281 -168 TCCTGTCACACAGGATCCATGTTCCCTCTGCTGAATCT 7 30 1 CAATATCCTC 0.99134 -170 ATCATTGTAGCACGATAGACTAAGCCTTATATCACTGC 7 116 1 CAATAACCTT 0.905137 -84 TAATTATAATATACACTACCTCTATAGATTCT 12 5 1 TAATATCCTC 0.938687 -73 GCGATATGAACACCATATGATGAACCTCAGAATGTGAT 13 87 0 CAATGACCTC 0.957804 -136 CCATTTCAATCAGCACAGAATGTACCTCATTGAAGAGG 20 41 1 CAACATCCTC 0.973272 -152 TCCACCGGAGCAATATTTAAAAACCCTCACCTTAAAAA 20 131 1 CAATAACCTC 0.988433 -62 GGTTAATATTCAGCGTTTATCATTCCTCAATTGAAAAA 21 98 0 CAGTATCCTC 0.987225 -123 ** ** * * **** Masking position 2 Map Score: 4.82257 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 52 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 GAATTAACCAGGGAAATTAAACGGGGT 6 6 0 GGGATTAAAC 0.911783 -70 ATTGTGATAAGTGTGGTGAAATT 12 65 1 GTGTTGAAAT 0.704126 -13 TGAACTCCATGTGAGAAGAAACCTATCAGATC 13 157 1 GTGAAGAAAC 0.819047 -66 CTGTGATCCTGTGAGAATAACTATGAAATGAG 15 22 1 GTGAATAACT 0.85517 -111 TTGAAATTAGGTGTGAATAAATAAACGGTGAT 16 15 1 GTGTATAAAT 0.891289 -25 AATGCCTGATGTGACTATAAATCTTTTCAT 17 9 0 GTGAATAAAT 0.927698 -32 TTGCTCCGGTGGATCTTTAAACCCCTAGTAAT 20 112 0 GGATTTAAAC 0.544743 -81 TTTAAGGTGAGGGTTTTTAAATATTGCTCCGG 20 135 0 GGGTTTAAAT 0.844634 -58 CATCACCTTGGTAAGAATAACTAATGTTATTG 20 169 0 GTAAATAACT 0.517023 -24 TTTCAATTGAGGAATGATAAACGCTGAATATT 21 100 1 GGAAATAAAC 0.652125 -121 ATTAATATAGGTGCATTTAAATTTATATGTAG 21 173 1 GTGCTTAAAT 0.749865 -48 ATACCTCCCGGTGAAGTTAAACCTACATATAA 21 195 0 GTGATTAAAC 0.939734 -26 ATTAAGGTTTGTGATTTTAACTGATAATCTTT 23 27 0 GTGATTAACT 0.85517 -79 ACCTTAATATGTGTTGATAAACAATTAAAATT 23 51 1 GTGTATAAAC 0.908792 -55 **** ****** Masking position 9 Map Score: 7.81092 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 110 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 AAGGTATAATATTCCTCAGGAACTCAACAC 1 25 0 ATTCCTCAGG 0.94762 -171 CCAGCGGAATATTCCCCAGGAACACGGAAG 1 88 0 ATTCCCCAGG 0.989519 -108 CCTGGGGAATATTCCGCTGGAGGGGTGCTG 1 98 1 ATTCCGCTGG 0.980403 -98 CCCCAGATAGAGTTCCCTGGAAAACCAGCA 1 123 0 AGTTCCCTGG 0.956071 -73 CCCTGAAGGATTTCCCCTGGAGGGTCAGGG 1 161 1 TTTCCCCTGG 0.977507 -35 ACCCCGTTTAATTTCCCTGGTTAATTCAGG 6 11 1 ATTTCCCTGG 0.983477 -65 ********** Masking position 3 Map Score: 6.0558 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 62 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 CCGCTGGAGGGGTGCTGGTTTTCCAGGGAA 1 111 1 GGTGCTGGTT 0.980169 -85 TCCCCTGGAGGGTCAGGGTTTGAGATAATT 1 173 1 GGTCAGGGTT 0.914178 -23 ACCTCCCGTGAGTGCTGGTTGAG 3 4 0 AGTGCTGGTT 0.904501 -20 TTTAAAAGGTTGTGAAGGTTA 9 39 1 TGTGAAGGTT 0.932571 -11 ACAGAAAATATGTGGAGGTTTTTGT 18 11 1 TGTGGAGGTT 0.861693 -15 AGGTACATTCTGTGCTGATTGAAATGGAAA 20 38 0 TGTGCTGATT 0.727699 -155 TTGTTTTTAAGGTGAGGGTTTTTAAATATT 20 142 0 GGTGAGGGTT 0.9847 -51 CTATTAATTTGGAGAGGGTTATTGA 22 6 0 GGAGAGGGTT 0.920215 -105 ********** Masking position 9 Map Score: 4.06281 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 222 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TGATAAGGTGAATCAGAAACTTTATTCTTACCGG 6 48 1 AACAACTTTA 0.942244 -28 ATCACTGCAGCACCATAGACTTTATGTGTTTCAC 7 146 1 CACAACTTTA 0.980307 -54 GCATCACACCCCCTAGATCAGTGCC 8 38 0 CACAACCCTA 0.937396 -15 TAACCTTCACAACCTTTTAAATGTTGGA 9 32 0 CTCAACTTTT 0.712622 -18 GGGTTAACCCCATCAAATCCTTTATCCTTTTTCT 19 13 1 CACAACTTTA 0.980307 -155 TGAAGAGGTTCAGGAGATCCCTTAAGGGTCATCA 20 71 1 CAGAACCTTA 0.903021 -122 TTCATATTTTAAGCACCATCCTTAAATAATTTAA 21 38 0 AACACCCTTA 0.830721 -183 TGCGGCCTATCATCAAACTCTTTTCATATTTTAA 21 60 0 CACAACTTTT 0.940228 -161 TATCAGTTAAAATCACAAACCTTAATATGTGTTG 23 33 1 AACAACCTTA 0.954553 -73 ** ** * ***** Masking position 5 Map Score: 3.74849 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 116 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GTATAATATTCCTCAGGAACTCAACACTCT 1 22 0 CCTCAGGAAC 0.948966 -174 GCGGAATATTCCCCAGGAACACGGAAGGCC 1 85 0 CCCCAGGAAC 0.967375 -111 GGCGCTGACACCCCAGATAGAGTTCCCTGG 1 133 0 CCCCAGATAG 0.908957 -63 AGGGGAAATCCTTCAGGGCGCTGACACCCC 1 149 0 CTTCAGGGCG 0.856356 -47 AAAAACATGGCCTCAGATTCAGCAGAGGGA 7 52 0 CCTCAGATTC 0.796619 -148 ATAAACCTTGCCACAGAGACCTGTCACAGA 7 86 0 CCACAGAGAC 0.845001 -114 GTGCCAGTTCCTCCAGGACCATCATGAGCC 8 13 0 CTCCAGGACC 0.898257 -40 CTCCAGTGACCCTTGAATGG 10 1 1 CTCCAGTGAC 0.793666 -40 CTGCAAAGCACTCCAGAGAGCACCTCAAGC 11 182 0 CTCCAGAGAG 0.939397 -59 ATATGATGAACCTCAGAATGTGATATGCCG 13 81 0 CCTCAGAATG 0.88303 -142 ATATGAAAAACTTCAGAATGAACTGAATTT 23 78 0 CTTCAGAATG 0.798755 -28 ********** Masking position 5 Map Score: 5.2715 Number of sites scoring better than the average of aligned sites = 1179 Number in coding regions = 1133 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 CCGCCACCTGTTTTACTTATAATC 14 26 0 CACCTGTTTT 0.965994 -14 TATTTATTCACACCTAATTTCAATAAT 16 8 0 CACCTAATTT 0.95041 -32 CAAAAACCTCCACATATTTTCTGT 18 5 0 CACATATTTT 0.923036 -21 TGGAAGTTAACACCAATTTTATATTGTCAT 19 132 1 CACCAATTTT 0.950412 -36 ATTGTCATTGCAACTATTTTCCTA 19 154 1 CAACTATTTT 0.923036 -14 AATTTAAATGCACCTATATTAATATTGACG 21 166 0 CACCTATATT 0.95041 -55 ********** Masking position 2 Map Score: 2.52069 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 14 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 TCGCTGCAGTCATCCATGGAA 2 2 1 CGCTGCAGTC 0.776715 -63 ACAGGATGACCACTGCAGACATGGG 7 6 0 CACTGCAGAC 0.647653 -194 TCCATGTTCCCTCTGCTGAATCTGAGGCCA 7 45 1 CTCTGCTGAA 0.815707 -155 AGCCTTATATCACTGCAGCACCATAGACTT 7 138 1 CACTGCAGCA 0.725863 -62 GATGAATACACTTTGCAGTGTTTGAGAGCT 11 155 1 CTTTGCAGTG 0.801194 -86 TTGAGGTGCTCTCTGGAGTGCTTTGCAGCC 11 184 1 CTCTGGAGTG 0.740137 -57 CTCTGGAGTGCTTTGCAGCCTAATAATCTA 11 194 1 CTTTGCAGCC 0.955907 -47 TCTATTAACTCTTTGCTGTCCAAGACAATA 15 76 0 CTTTGCTGTC 0.913142 -57 ********** Masking position 4 Map Score: 1.84662 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 377 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 ********** No masking Map Score: -6.1935e-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: -6.1935e-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: -6.1935e-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