AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_mthe_reg_100.orf -o00350_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 MTH52 189 aspartate aminotransferase related protein #2 MTH147 23 phenylacrylic acid decarboxylase #3 MTH148 47 conserved protein #4 MTH150 75 conserved protein #5 MTH1348 139 precorrin-2 methyltransferase #6 MTH1514 125 precorrin-6Y methylase #7 MTH1587 31 histidinol-phosphate aminotransferase #8 MTH1591 30 phosphonopyruvate decarboxylase #9 MTH1592 21 conserved protein #10 MTH1593 205 ribosomal protein S3a #11 MTH1601 246 aspartate aminotransferase #12 MTH1694 207 aspartate aminotransferase related protein #13 MTH1894 34 aspartate aminotransferase homolog #14 MTH1895 170 conserved protein Motif number 1 GGAATTATAAACCCCAGAAAACAGAAAAA 1 10 0 ACCCCAGAAA 0.808466 -180 TGAATCCCCAGCCTGTGAAGAAGCCGGATC 1 88 0 GCCTGTGAAG 0.893843 -102 TATCATGTAGTCCACTGGAGTTAATAAAAA 1 127 0 TCCACTGGAG 0.852599 -63 AGTTAATTCAACACGAGAAGAATGATATTA 1 155 0 ACACGAGAAG 0.728923 -35 TGTTGAATTAACTTCTGGAGGATAAATC 1 172 1 ACTTCTGGAG 0.568389 -18 CCGTTAATCTGTTCCAGGAGGTTTCTGTCC 3 20 0 GTTCCAGGAG 0.734402 -28 TTTAGAGAGTGCCACAGAAAAATAATGATA 5 42 1 GCCACAGAAA 0.811779 -98 TCTGGATATTTCCAGAGAAGGATGACCAGA 5 83 1 TCCAGAGAAG 0.834447 -57 GTTAACTCAGGTCACTGGAGAG 7 3 0 GTCACTGGAG 0.9123 -29 TGGGAGCTGGAGCTCAGGAGCCTGATTCAG 11 60 1 AGCTCAGGAG 0.884167 -187 CCTGATTCAGGTCCCTGAAGCCGCGATCCA 11 80 1 GTCCCTGAAG 0.926638 -167 CCAGTCATGGGGCCCTGAAGAGGTGATTAA 11 114 0 GGCCCTGAAG 0.925266 -133 AACTTTGTTTACCAGAGGAGCCTCTGTAAT 12 62 0 ACCAGAGGAG 0.953771 -146 CCTCGGGTAGGTAAGAGAAGCCTTCTTCTC 12 154 1 GTAAGAGAAG 0.493159 -54 TTATCACATCAGCACAGGAGTATCCATGCG 12 187 0 AGCACAGGAG 0.928296 -21 TTTATTTTTGATCTCAGAAGATTCTC 13 7 0 ATCTCAGAAG 0.872516 -28 ATCATCAAGAACCCGAGAAGGTTGAT 14 155 1 ACCCGAGAAG 0.961614 -16 ********** Masking position 9 Map Score: 14.6296 Number of sites scoring better than the average of aligned sites = 2339 Number in coding regions = 2230 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 2 TGTTTTCCAGCAGTGATCCGGCTTCTTCACAGG 1 74 1 CGGTCCGGCT 0.935579 -116 CTTCACAGGCTGGGGATTCAGCACAGCAATTTT 1 98 1 TGGTTCAGCA 0.916575 -92 CAGATATTCACTGGGTCTCAGCAATCTCTCCAT 6 68 0 CGGCTCAGCA 0.984867 -58 AATCAGGCTCCTGAGCTCCAGCTCCCACCAGGA 11 54 0 CGGTCCAGCT 0.987199 -193 GTCCCTGAAGCCGCGATCCATCAGTTAATCACC 11 90 1 CGGTCCATCA 0.982833 -157 ATCACCTCTTCAGGGCCCCATGACTGGCTGATT 11 117 1 CGGCCCATGA 0.971429 -130 CCATGACTGGCTGATTTTCAGGTCGGATTTACT 11 134 1 CGTTTCAGGT 0.775182 -113 TGATGGCTGGCCGGGACTCATGTAAATCTTTTT 11 166 1 CGGCTCATGT 0.961089 -81 GATTTTATTACAGAGGCTCCTCTGGTAAACAAA 12 56 1 CGGCTCCTCT 0.865662 -152 TGGAGTTTAATTGAGGTTCAGCCTCGGGTAGGT 12 133 1 TGGTTCAGCC 0.771801 -75 TGCTAGACAGCGGAGATTAATGAACCTTCAACC 14 42 1 CGGTTAATGA 0.7191 -129 ATTGTATTCCCGGAGTTCCATGAGATTATATTT 14 119 0 CGGTCCATGA 0.976376 -52 * * * ******* Masking position 3 Map Score: 10.2954 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 583 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 AGGCTGGGGATTCAGCACAGCAATTTTTAT 1 104 1 TTCAGCACAG 0.932639 -86 AAAAAATCAGGACAGAAACCTCCTG 3 6 1 ATCAGGACAG 0.95624 -42 ATTCCATCAAATCAGCACGGAGGCAGATAT 6 94 0 ATCAGCACGG 0.903082 -32 TCTCGGTTAACTCAGGTCACTGGAGAG 7 8 0 CTCAGGTCAC 0.952208 -24 TCAAATGGATCGGGACCCCTC 9 9 1 ATCGGGACCC 0.911851 -13 TTCATGACCACACAGCACCCCAAACCACCA 10 33 1 CACAGCACCC 0.825129 -173 GCTCCTGAGCTCCAGCTCCCACCAGGAGAA 11 51 0 TCCAGCTCCC 0.807941 -196 GGAGCTGGAGCTCAGGAGCCTGATTCAGGT 11 62 1 CTCAGGAGCC 0.862554 -185 AGGAGCCTGATTCAGGTCCCTGAAGCCGCG 11 75 1 TTCAGGTCCC 0.974792 -172 TAATCACCTCTTCAGGGCCCCATGACTGGC 11 115 1 TTCAGGGCCC 0.945711 -132 CTGGCTGATTTTCAGGTCGGATTTACTGAT 11 140 1 TTCAGGTCGG 0.896584 -107 CTGTAATAAAATCAGGCCACATTATCCTAC 12 39 0 ATCAGGCCAC 0.901564 -169 TTTATCACATCAGCACAGGAGTATCCAT 12 190 0 ATCAGCACAG 0.932639 -18 ********** Masking position 3 Map Score: 11.9523 Number of sites scoring better than the average of aligned sites = 811 Number in coding regions = 769 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 CCCGCATAACTGGCTGTTCATATTC 10 6 1 ATAACTGGCT 0.979316 -200 CACCGTAAAAACAGCTGGATTTAACATAAA 10 166 0 ACAGCTGGAT 0.954245 -40 TCAGGGCCCCATGACTGGCTGATTTTCAGG 11 126 1 ATGACTGGCT 0.986746 -121 GGATTTACTGATGGCTGGCCGGGACTCATG 11 158 1 ATGGCTGGCC 0.989801 -89 ACCATGACTGGACTGTTTTTAGC 12 4 1 ATGACTGGAC 0.954245 -204 ACATTATCCTACAGCTGGCTAAAAACAGTC 12 21 0 ACAGCTGGCT 0.984056 -187 ********** Masking position 6 Map Score: 5.93481 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 44 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 5 GTCTTGCCCCGTTAATCTGTTCCAGGAGGT 3 28 0 CTTAATCTGT 0.906976 -20 AGATCATAAATCTAGGAAGGTGGGT 8 5 1 CTAAATCTAG 0.857321 -26 TAAGGGAGTATTTAAATCTTGACATGGTGGT 10 56 0 TTAAATCTTG 0.947793 -150 TGTATGTAACTCTAAATCATGGTTAACCAGT 10 116 1 TTAAATCATG 0.878456 -90 TATATCACCTTAATCTTTAACACCGTAA 10 188 0 CTTAATCTTT 0.859429 -18 AAGAATGATATATAAATGTGGATAAAGTTAT 11 14 0 TTAAATGTGG 0.77174 -233 GCTTCAGGGACCTGAATCAGGCTCCTGAGCT 11 70 0 CTGAATCAGG 0.742725 -177 CCGGGACTCATGTAAATCTTTTTAAATGGAC 11 176 1 TTAAATCTTT 0.869622 -71 CTGTATCTATTTTTAATCTGTCCATTTAAAA 11 195 0 TTTAATCTGT 0.879013 -52 ATGAAATCCACTTTAATCTGGAGGTTTT 11 229 1 CTTAATCTGG 0.963676 -18 CAGCTGAATTTATAAATCATGCTAGACAGCG 14 23 1 TTAAATCATG 0.878477 -148 * ********* Masking position 6 Map Score: 7.14361 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 69 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 TATAATTCCTTTTTTAACAGGGTATCCCTGAGAA 1 31 1 TTTTAAGGTA 0.988114 -159 GGACCTATTTAAGGGGGTGGAACTATATA 5 6 1 TTTTAAGGTG 0.962376 -134 TATGGAATACTCTATAATAGGATAAGGGAGTATT 10 75 0 TTATAAGGTA 0.94523 -131 AAAAAATTCATATTTAACTGGTTAACCATGATTT 10 129 0 TTTTAAGGTA 0.988113 -77 AATCCAGCTGTTTTTACGGTGTTAAAGATTAAGG 10 175 1 TTTTACTGTA 0.874651 -31 CATGTAAATCTTTTTAAATGGACAGATTAAAAAT 11 184 1 TTTTAAGGCA 0.962376 -63 TTAAGAGGTTTGTTTAATATGGTATAAGAAACCC 12 94 1 TTTTAATGTA 0.957765 -114 * ***** ** ** Masking position 6 Map Score: 4.1353 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 CTGGAAATATCCAGACCCGCCTTTATTATCAT 5 66 0 CCAACCCCCT 0.990623 -74 AGAAGGATGACCAGACCATCATCATGTCTACA 5 98 1 CCAACCACAT 0.994587 -42 AGAGAGTGTCCCATACCAACATTTTATTATAA 6 33 0 CCAACCACAT 0.994587 -93 ACACAGCACCCCAAACCACCATGTCAAGATTT 10 42 1 CCAACCACAT 0.994587 -164 TAAAATCAGGCCACATTATCCTACAGCTGGCT 12 31 0 CCAATTACCT 0.913865 -177 ACTTTGTTTACCAGAGGAGCCTCTGTAATAAA 12 59 0 CCAAGGACCT 0.958858 -149 *** **** *** Masking position 5 Map Score: 4.61427 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 49 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 8 TTTATTAACTCCAGTGGACTACATGATAATATCA 1 129 1 CCAGGGTACT 0.763262 -61 GATTTATCCTCCAGAAGTTAATTCAACACGAGAA 1 166 0 CCAGAGAATC 0.991185 -24 GCCACCGGCTCCATGAATATATACTAGAAGCACC 4 13 1 CCATAATATC 0.836526 -63 ACATACACCGCCAGTATGGAATACTCTATAATAG 10 89 0 CCAGATAATC 0.926249 -117 CCAGCTCCCACCAGGAGAAAACCCAAAGAATGAT 11 36 0 CCAGAGAACC 0.982135 -211 AAGCCGCGATCCATCAGTTAATCACCTCTTCAGG 11 97 1 CCATAGAATA 0.918898 -150 TCCCGGCCAGCCATCAGTAAATCCGACCTGAAAA 11 148 0 CCATAGAATC 0.988682 -99 TTAAACTGCTCCATGGGGCAATACCATGTGAGGT 14 72 0 CCATGGAATC 0.977116 -99 TCCCGGAGTTCCATGAGATTATATTTAGGTTCAT 14 111 0 CCATAGTATT 0.912895 -60 **** ** *** * Masking position 11 Map Score: 5.22092 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 174 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 TTTATTAACTCCAGTGGACTACATGATAAT 1 129 1 CCAGTGGACT 0.811769 -61 TAGTATATATTCATGGAGCCGGTGGCGA 4 9 0 TCATGGAGCC 0.949329 -67 CTCTCCAGTGACCTGAGTTAACCG 7 5 1 CCAGTGACCT 0.873712 -27 GAGCTGGAGCTCAGGAGCCTGATTCAGGTC 11 63 1 TCAGGAGCCT 0.803654 -184 GATCGCGGCTTCAGGGACCTGAATCAGGCT 11 78 0 TCAGGGACCT 0.977062 -169 AATCAGCCAGTCATGGGGCCCTGAAGAGGT 11 120 0 TCATGGGGCC 0.948357 -127 TGGTATTGCCCCATGGAGCAGTTTAAGTGC 14 80 1 CCATGGAGCA 0.849976 -91 ATATTTAGGTTCATGGCACTTAAACTGCTC 14 95 0 TCATGGCACT 0.884972 -76 AAATATAATCTCATGGAACTCCGGGAATAC 14 119 1 TCATGGAACT 0.95463 -52 ********** Masking position 3 Map Score: 3.83915 Number of sites scoring better than the average of aligned sites = 1746 Number in coding regions = 1688 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 AATTCTTTCTCAGGGATACCCTGTTAAAAAAGG 1 38 0 CGGATACCTG 0.774062 -152 CGGATCACTGCTGGAAAACAAAAAATTCTTTCT 1 61 0 CGGAAACAAA 0.936344 -129 GAGAGTGCCACAGAAAAATAATGATAATAAAGG 5 46 1 CGAAAATATG 0.814283 -94 ATAAGTAGTGCCGGGATATTATAATAAAATGTT 6 15 1 CGGATATATA 0.876296 -111 TCATATTTAACTGGTTAACCATGATTTAGAGTT 10 123 0 CGGTAACATG 0.960142 -83 AGAGGCTCCTCTGGTAAACAAAGTTTATTAAGA 12 67 1 CGGAAACAAG 0.981789 -141 CATGGAACTCCGGGAATACAATGTCATCATCAA 14 130 1 CGGATACATG 0.9896 -41 * ** **** *** Masking position 8 Map Score: 0.947288 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 169 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 CAAAAAATTCTTTCTCAGGGATACCCTGTT 1 46 0 TTTCTCAGGG 0.879771 -144 AGAAGCCGGATCACTGCTGGAAAACAAAAA 1 70 0 TCACTGCTGG 0.898088 -120 CGTGTTGAATTAACTTCTGGAGGATAAATC 1 170 1 TAACTTCTGG 0.831186 -20 TATGTAACTCTAAATCATGGTTAACCAGTT 10 118 1 TAAATCATGG 0.790914 -88 TTCTTTGGGTTTTCTCCTGGTGGGAGCTGG 11 40 1 TTTCTCCTGG 0.962733 -207 AAGAGGTGATTAACTGATGGATCGCGGCTT 11 97 0 TAACTGATGG 0.959541 -150 CAGGTCGGATTTACTGATGGCTGGCCGGGA 11 152 1 TTACTGATGG 0.959541 -95 CCTTCTTCTCTTTCGCATGGATACTCCTGT 12 174 1 TTTCGCATGG 0.879771 -34 ACCTAAATATAATCTCATGGAACTCCGGGA 14 115 1 AATCTCATGG 0.831569 -56 ********** Masking position 9 Map Score: 4.01672 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 267 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 CCTGGAACAGATTAACGGGGCAAGAC 3 32 1 ATTAACGGGG 0.948163 -16 GGACCTATTTAAGGGGGTGGAACTAT 5 7 1 ATTTAAGGGG 0.962771 -133 AAATAATGATAATAAAGGCGGGTCTGGATA 5 61 1 AATAAAGGCG 0.96908 -79 CTACAGAGTTATTAAAGGTGTTCTA 5 125 1 ATTAAAGGTG 0.963482 -15 CGGTGTTAAAGATTAAGGTGATATA 10 191 1 GATTAAGGTG 0.730621 -15 AAACCTCCAGATTAAAGTGGATTTCATAAC 11 226 0 ATTAAAGTGG 0.885198 -21 ATCAAAAATAAATAAAGGCG 13 25 1 AATAAAGGCG 0.96908 -10 ********** Masking position 5 Map Score: 4.4309 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 49 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ********** No masking Map Score: 3.32777e-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: 3.32777e-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: 3.32777e-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