AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_mthe_reg_100.orf -o00051_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 MTH332 119 LPS biosynthesis RfbU related protein #2 MTH338 190 LPS biosynthesis RfbU related protein #3 MTH343 48 rhamnosyl transferase #4 MTH347 60 O-antigen transporter #5 MTH348 194 rhamnosyl transferase #6 MTH447 109 sensory transduction regulatory protein #7 MTH448 74 unknown #8 MTH449 38 unknown #9 MTH661 119 ammonium transporter #10 MTH662 61 nitrogen regulatory protein P-II #11 MTH663 205 ammonium transporter #12 MTH839 253 unknown #13 MTH1041 195 triosephosphate isomerase #14 MTH1405 82 DNA polymerase delta small subunit #15 MTH1406 48 fuculose-1-phosphate aldolase #16 MTH1584 112 phosphomannomutase #17 MTH1591 30 phosphonopyruvate decarboxylase #18 MTH1592 21 conserved protein #19 MTH1593 205 ribosomal protein S3a #20 MTH1759 70 mannose-1-phosphate guanyltransferase #21 MTH1762 159 DNA mismatch recognition protein MutS Motif number 1 AGGTATAAACTACAGGAAAGCACCTAAGAT 1 35 1 TACAGGAAAG 0.761639 -85 TCCAGTCCAGTCCAGTCCAGTCCATCCTAT 5 105 0 TCCAGTCCAG 0.975838 -90 TCCAGTCCAGTCCAGTCCAGTCCAGTCCAG 5 115 0 TCCAGTCCAG 0.975838 -80 CTTTTATCAGTCCAGTCCAGTCCAGTCCAG 5 125 0 TCCAGTCCAG 0.975838 -70 GTCCAGGACATTGAAGTCAAA 8 28 0 TCCAGGACAT 0.9525 -11 ACCGGTGTCATCCAGGGCATGGTTCATACC 12 184 1 TCCAGGGCAT 0.988722 -70 GCCTGTAATATCCAGCGCATCCCCACATAG 13 81 0 TCCAGCGCAT 0.968767 -115 CGCTGGATATTACAGGCAAATTCATTCATG 13 94 1 TACAGGCAAA 0.720643 -102 AAAACCACCTTACAGGGCAGTGAAGGATTA 14 61 1 TACAGGGCAG 0.968616 -22 TCAAATATTATCCAGTGAATGGGGCTGTTA 16 89 1 TCCAGTGAAT 0.944244 -24 AGTATTTTTTTCCAGCGAATATGCAATTAC 20 27 0 TCCAGCGAAT 0.933511 -44 TCCATATATATCCAGGGAAATTTATAGTTG 21 138 1 TCCAGGGAAA 0.945247 -22 ********** Masking position 4 Map Score: 17.2248 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 391 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 TCAAAATGCGAGTGGGGGGTAAAGACTGCTAAAA 2 62 0 AGTGGGTAAG 0.937286 -129 GATTTTTACTGCTGTAGGTTTAAGGGAGGAATAG 5 70 1 GCTGGGTAAG 0.972266 -125 CTTTGATGTCACTGCAGAATAAGGTTTAATGTGA 6 24 0 ACTGGATAGG 0.779891 -86 AACCGCTATCACTGAGGACTAATGTCTGGACATT 6 68 0 ACTGGATATG 0.944413 -42 AGGGACGAACACACCGGGGTAATGGAGCATGAAC 12 68 0 ACACGGTATG 0.817301 -186 AACGCTGACCACTCCGGGCTGATGACAGGGATGT 12 119 0 ACTCGGTATG 0.976764 -135 AATGCAGAAAGCTGTTGGATGATGTTAAACCAGT 13 36 0 GCTGGGTATG 0.98996 -160 CTTACAGGGCAGTGAAGGATTAAA 14 69 1 AGTGGGTAAA 0.654095 -14 GAACCCTGCAACTGTATGTTGATGTAATCCAAG 15 26 1 ACTGTGTATG 0.974746 -23 CCCGCATAACTGGCTGTTCATATTCATGACCA 19 9 1 ACTGTGTATA 0.830037 -197 GGTTTGGGGTGCTGTGTGGTCATGAATATGAACA 19 25 0 GCTGTGTATG 0.96592 -181 AGTATTCCATACTGGCGGTGTATGTAACTCTAAA 19 98 1 ACTGGGGATG 0.954913 -108 TCACATCGAAGGTCGCTGCTGATGGGTATGGCAG 21 16 0 GGTCTGTATG 0.735284 -144 **** ** * *** Masking position 12 Map Score: 9.72878 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 392 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 CATTTGGACTTGTAGTTATTACGAAAACCTC 2 150 0 TGTAGTATTA 0.840511 -41 GAGTTAAGCGTGAGGAGATGATGCC 3 34 1 TGAGGGATGA 0.94354 -15 TCCTCGAACATGGAGAGATGAAAA 5 181 1 TGGAGGATGA 0.864874 -14 GACGTCAGGCTGAAGTTATGATGGTACACGC 7 54 1 TGAAGTATGA 0.941451 -21 TTTCAGTAATTGAGGTTATTATCTAAACTTG 11 41 1 TGAGGTATTA 0.955825 -165 TTTGATGAATTCAGGGTATGAACCATGCCCT 12 197 0 TCAGGTATGA 0.853946 -57 CCCCACATAGTGAAGGTGTTAAATGCAGAAA 13 60 0 TGAAGTGTTA 0.866783 -136 TCATACGGAGTGAAGGTCTGACTTTATCCAT 16 42 1 TGAAGTCTGA 0.770282 -71 ATCCAGTGAATGGGGCTGTTAAAAA 16 98 1 TGGGGTGTTA 0.895971 -15 TGGGGTGCTGTGTGGTCATGAATATGAACAG 19 24 0 TGTGGCATGA 0.73842 -182 TTCTGGTTATTATAATGTAATT 20 2 1 TCTGGTATTA 0.65724 -69 TCAGAAAGAGTGGGGATATTAGGTGCAATAA 21 51 0 TGGGGTATTA 0.939047 -109 TATTCTCTGTTGAAGCGGTTACTCCCAGATT 21 87 0 TGAAGGGTTA 0.784365 -73 ***** ***** Masking position 11 Map Score: 8.74905 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 361 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 CATTTTGAGGGGCTACAGGAGTTGCTCAGATTG 2 88 1 GGTAGGAGTT 0.975293 -103 CATATTCTCCGGATCCAGGTGTTCATGCTCCAT 12 48 1 GGTAGGTGTT 0.986886 -206 CATCCCCACATAGTGAAGGTGTTAAATGCAGAA 13 61 0 TATAGGTGTT 0.809871 -135 GTGCGGGAGTTGTTGAAGGGGTTCATGAATGAA 13 114 0 TGTAGGGGTT 0.939964 -82 TCTCATAGTATGGTTGAGGTGTATTATAAAATA 13 160 0 TGTAGGTGTA 0.916757 -36 TACAGTTGCAGGGTTCAGGTGTATATAACAT 15 9 0 GGTAGGTGTA 0.967716 -40 ATTATCCAGTGAATGGGGCTGTTAAAAA 16 95 1 GATGGCTGTT 0.808545 -18 TTGACATGGTGGTTTGGGGTGCTGTGTGGTCAT 19 36 0 GGTGGGTGCT 0.929843 -170 CTCTATAATAGGATAAGGGAGTATTTAAATCTT 19 67 0 GGTGGGAGTA 0.936327 -139 CGCTGCTGATGGGTATGGCAGTTATA 21 4 0 GGTGGCAGTT 0.934979 -156 AAGTATTCTCTGTTGAAGCGGTTACTCCCAGAT 21 88 0 TGTAGCGGTT 0.859121 -72 ** * ******* Masking position 4 Map Score: 8.4225 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 329 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GATTAAAATAGCATCATTTATAAAGGTATAAAC 1 12 1 GATTTTATAA 0.967165 -108 GTCTACTCCAGGATCTTTTATCAGTCCAGTCCA 5 136 0 GATTTTATCA 0.966524 -59 ATCCTTAACCGGATTTCTTATAAGTACTTCTGT 10 32 0 GATCTTATAA 0.886652 -30 CAGTATAACTGTATATTTAATAAATTACTTACA 12 231 0 GATTTAATAA 0.948312 -23 GGATGTCACAGCATATTTTATAATACACCTCAA 13 147 1 GATTTTATAA 0.967166 -49 CACTCCGTATGAATTTTTAATCACATTACCTCA 16 21 0 GATTTAATCA 0.947364 -92 GATAATATTTGAATTGTTAATCACCAATATGGA 16 68 0 GATTTAATCA 0.947356 -45 CGCCAGTATGGAATACTCTATAATAGGATAAGG 19 82 0 GATTCTATAA 0.886675 -124 * ** ******* Masking position 10 Map Score: 6.00517 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 17 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 CCTATGAGGAATGCCGGGACCTCCAGAAGTG 4 9 0 ATGCGGGACC 0.983875 -52 GTTTAATGTGACGCCGTGACCAGA 6 2 0 ACGCGTGACG 0.909899 -108 AAACCTTATTCTGCAGTGACATCAAAGTATCAG 6 31 1 CTGCGTGACC 0.983875 -79 AGTGGCAGACCTGCGAGGGCTGCTTCTTAA 12 8 0 CTGCAGGGCC 0.851732 -246 CGCAGGTCTGCCACTGTGGCAACATATTCTCCG 12 26 1 CCACGTGGCC 0.967559 -228 GGAGCCACTTCCACAGGGACGAACACACCGGGG 12 83 0 CCACGGGACA 0.930492 -171 ACGAGCTACTCCACTGGGACCTCATGGGAACGC 12 148 0 CCACGGGACC 0.991727 -106 GCCCTGGATGACACCGGTACAACGAGCTACTCC 12 169 0 ACACGGTACC 0.856768 -85 ATTATAAAATATGCTGTGACATCCGTGCGGGAG 13 138 0 ATGCGTGACC 0.968805 -58 **** ***** * Masking position 4 Map Score: 4.62179 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 561 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 CTTTACCCCCCACTCGCATTTTGAGGGGCTACAGGA 2 72 1 CACCATTGAG 0.945077 -119 TCAATCATCCTTTCTCTGATGAGTTAATCCC 4 40 0 CATCTTCGAG 0.97038 -21 TTTTCATCTCTCCATGTTCGAGGATCTGCATTC 5 172 0 CTCCTTTGAG 0.981353 -23 CATCATCTTACTCTCATTGTCGGAAGTTACCTTCCT 11 125 1 CTCCTTCGAG 0.990392 -81 CGGAAGTTACCTTCCTATTTCCGACTATGATATAAA 11 145 1 CTTCTTCGAT 0.911974 -61 TAATAAATTACTTACAGTTTTTGATGAATTCAGGGT 12 211 0 CTTCTTTGAG 0.963892 -43 CATTTTAAAACTTTCTGAATTAGATGTTAAAAACCA 14 32 1 CTTCATTGAG 0.933546 -51 ACCTAATATCCCCACTCTTTCTGAAGTAAAATCTGG 21 58 1 CCCCTTCGAG 0.974232 -102 GAATACTTTCCACACGCACTCTGAATCCATATATAT 21 113 1 CACCATCGAT 0.869413 -47 *** * * ** ** * Masking position 10 Map Score: 6.56199 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 62 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CTATTGGCTAATTTGAATCTTAGGTGCTTTC 1 50 0 ATTGAATCTT 0.930751 -70 AAGTAATATTATTTAAACTTTTCGTATGATG 5 24 1 ATTAAACTTT 0.711704 -171 TGATGCTGATATATAAATCTTTCGGATATAG 11 99 0 ATTAAATCTT 0.893936 -107 TCCGACTATGATATAAATTGTTGGAGAGAAA 11 164 1 ATTAAATTGT 0.852641 -42 AATGTTTACAATTTAATTTTTCACTGGTTTA 13 14 1 ATTAATTTTT 0.624854 -182 CCTTCACTCCGTATGAATTTTTAATCACATT 16 27 0 GTTGAATTTT 0.797439 -86 ACTGGATAATATTTGAATTGTTAATCACCAA 16 74 0 ATTGAATTGT 0.902222 -39 ATAAGGGAGTATTTAAATCTTGACATGGTGG 19 57 0 ATTAAATCTT 0.893936 -149 AACCAGTTAAATATGAATTTTTTGAATTTAT 19 140 1 ATTGAATTTT 0.949691 -66 GCGACCTTCGATGTGAATTATTGCACCTAAT 21 34 1 ATTGAATTAT 0.771841 -126 ** ******** Masking position 6 Map Score: 4.00592 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 12 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 9 ACCTCATGTCCTCTTTTTACTAGGTGCTCG 2 125 0 CTCTTTTTAC 0.971257 -66 AGCCTGACGTCTCTTTATACTTGCTCTGAT 7 35 0 CTCTTTATAC 0.911273 -40 ATTATCTAAACTTGTTTTACTCAGCATACA 11 58 1 CTTGTTTTAC 0.930427 -148 AGTGGAGTAGCTCGTTGTACCGGTGTCATC 12 166 1 CTCGTTGTAC 0.959897 -88 TAATTTTTCACTGGTTTAACATCATCCAAC 13 27 1 CTGGTTTAAC 0.899991 -169 TTAAATCCAGCTGTTTTTACGGTGTTAAAG 19 172 1 CTGTTTTTAC 0.958674 -34 ********** Masking position 5 Map Score: 1.15655 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 8 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 TGATTTCTGGGTGAATCCATGAAAATATGT 2 30 1 GTGAATCCAT 0.950662 -161 TCTCTGATGAGTTAATCCCTATGAGGAATG 4 29 0 GTTAATCCCT 0.823857 -32 GGTTCATACCCTGAATTCATCAAAAACTGT 12 204 1 CTGAATTCAT 0.903216 -50 CTTTATTCATTGAGGTAATG 16 1 1 CTTTATTCAT 0.815819 -112 GAAGGTCTGACTTTATCCATATTGGTGATT 16 53 1 CTTTATCCAT 0.929156 -60 CACACGCACTCTGAATCCATATATATCCAG 21 123 1 CTGAATCCAT 0.972651 -37 ********** Masking position 5 Map Score: 0.458826 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 104 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TCAATCATCCTTTCTCTGATGA 4 49 0 AATCATCCTT 0.606675 -12 TTTTCATCTCTCCATGTTCGAGGAT 5 180 0 ATCTCTCCAT 0.612675 -15 GATAAACCTCCTTTATGGAACCG 6 97 0 AAACCTCCTT 0.969466 -13 ATCACTCTCCTTTTGGATGTGC 9 108 0 CACTCTCCTT 0.787279 -12 CTTAAATATCCTTAACCGGATTT 10 49 0 AAATATCCTT 0.760891 -13 TAGATGTTAAAAACCACCTTACAGGGCAGT 14 52 1 AAACCACCTT 0.962647 -31 GATTAACCCACCTTCCTAGATTTA 17 17 0 AACCCACCTT 0.96192 -14 ACAGCACCCCAAACCACCATGTCAAGATTT 19 44 1 AAACCACCAT 0.890638 -162 TATATCACCTTAATCTTTAAC 19 195 0 ATATCACCTT 0.805642 -11 ********** Masking position 10 Map Score: 2.20286 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 276 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 12 ACTCGCATTTTGAGGGGCTACAGGAGTTGC 2 83 1 TGAGGGGCTA 0.579519 -108 GAGTTAAGCGTGAGGAGATGATGCC 3 34 1 TGAGGAGATG 0.941093 -15 TCTCCATGTTCGAGGATCTGCATTCACTGT 5 167 0 CGAGGATCTG 0.844825 -28 TCCTCGAACATGGAGAGATGAAAA 5 181 1 TGGAGAGATG 0.807602 -14 GACGTCAGGCTGAAGTTATGATGGTACACG 7 54 1 TGAAGTTATG 0.833535 -21 TATTGGTGATTGCAGATATGTTAGGCACAT 9 84 1 TGCAGATATG 0.682846 -36 TTTCAGTAATTGAGGTTATTATCTAAACTT 11 41 1 TGAGGTTATT 0.645505 -165 AAGCAGCCCTCGCAGGTCTGCCACTGTGGC 12 16 1 CGCAGGTCTG 0.543861 -238 ACGAACACACCGGGGTAATGGAGCATGAAC 12 68 0 CGGGGTAATG 0.602523 -186 TTTGATGAATTCAGGGTATGAACCATGCCC 12 198 0 TCAGGGTATG 0.677075 -56 ACCTTCACTATGTGGGGATGCGCTGGATAT 13 74 1 TGTGGGGATG 0.800646 -122 CTTTATTCATTGAGGTAATGTGATTAAAAA 16 11 1 TGAGGTAATG 0.813368 -102 TCATACGGAGTGAAGGTCTGACTTTATCCA 16 42 1 TGAAGGTCTG 0.867697 -71 CATGGTGGTTTGGGGTGCTGTGTGGTCATG 19 35 0 TGGGGTGCTG 0.915215 -171 TCAGAAAGAGTGGGGATATTAGGTGCAATA 21 52 0 TGGGGATATT 0.599679 -108 ********** Masking position 9 Map Score: 2.3854 Number of sites scoring better than the average of aligned sites = 1560 Number in coding regions = 1456 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 13 ********** No masking Map Score: -6.88983e-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: -6.88983e-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: -6.88983e-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