AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_mthe_reg_100.orf -o00650_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 MTH139 269 heterodisulfide reductase HdrD related protein #2 MTH347 60 O-antigen transporter #3 MTH348 194 rhamnosyl transferase #4 MTH700 110 conserved protein #5 MTH702 27 acetyl-CoA synthetase related protein #6 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #7 MTH1116 146 glutamate decarboxylase #8 MTH1444 64 acetolactate synthase, large subunit #9 MTH1502 189 succinate dehydrogenase, flavoprotein subunit #10 MTH1602 63 acetolactate synthase, large subunit homolog #11 MTH1850_MTH1851 105 MTH1850: fumarate reductase, MTH1851: unknown Motif number 1 TGGTTATCTACTTCAGAGGATGTCTTGCAA 1 92 1 CTTCAGAGGA 0.799493 -178 AAGGGAGAGACTGCACGGGATATCCAGGGC 1 120 1 CTGCACGGGA 0.978876 -150 CTCAGAGCCGCAGGACTGGAATACAGAGTC 1 163 1 CAGGACTGGA 0.989014 -107 TTCAGATAAGCAGGACAGGAAGC 1 257 1 CAGGACAGGA 0.9865 -13 ATAGGATGGACTGGACTGGACTGGACTGGA 3 105 1 CTGGACTGGA 0.99595 -90 CTGGACTGGACTGGACTGGACTGGACTGGA 3 115 1 CTGGACTGGA 0.99595 -80 CTGGACTGGACTGGACTGGACTGATAAAAG 3 125 1 CTGGACTGGA 0.99595 -70 ATAAAAGATCCTGGAGTAGACAGTGAATGC 3 148 1 CTGGAGTAGA 0.905055 -47 CTCCTCAAGGCCGCACAGGAACTCCTCTAA 7 43 1 CCGCACAGGA 0.983122 -104 ATTAGAACGTCCGTAGAGGACCGGGTGATG 9 91 1 CCGTAGAGGA 0.866752 -99 ********** Masking position 5 Map Score: 20.2061 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 118 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 ATCTACTTCAGAGGATGTCTTGCAAGGGAGAG 1 97 1 GAGGATCTTG 0.603718 -173 AGAGACTGCACGGGATATCCAGGGCCACAGAG 1 125 1 CGGGATCCAG 0.921943 -145 GGGCCACAGAGAAGATACTCAGAGCCGCAGGA 1 146 1 GAAGACTCAG 0.88986 -124 TCTGCCTCTTCAAGGAACCCTGTCCTCAGAAG 1 223 0 CAAGGCCCTG 0.57693 -47 TGAGGAATGCCGGGACCTCCAGAAGTG 2 6 0 CGGGATCCAG 0.921943 -55 CCAGGCGGTGTCCCCTGTGTGGTAGTA 5 11 0 CGGTGCCCTG 0.677375 -17 ACCATGAAATGGAGAATCTCAGGTATCTGATT 6 15 1 GGAGACTCAG 0.891776 -215 AGGTTTTCAGCAAAATGCCCTGTCAGTCCCGG 6 95 0 CAAAACCCTG 0.788897 -135 CTCTGGTGAAGGGAACACCCTGATAATTTATT 6 125 1 GGGAACCCTG 0.962734 -105 CGGCCTTGAGGAGGAGTCTCTGCTCGGCCCTT 7 24 0 GAGGACTCTG 0.922864 -123 AAATAGTTTAGAGGAGTTCCTGTGCGGCCTTG 7 48 0 GAGGATCCTG 0.754854 -99 ACAGAACCCCCAGTGATCATTAT 9 2 1 CAGAACCCAG 0.875898 -188 TGACTCATATGAAAAACTTCAGAATGAACTGA 11 82 0 GAAAATTCAG 0.508911 -24 ***** ***** Masking position 12 Map Score: 10.8149 Number of sites scoring better than the average of aligned sites = 2259 Number in coding regions = 2164 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 3 CTTGCAAGACATCCTCTGAAGTAGATAACC 1 93 0 ATCCTCTGAA 0.947105 -177 CTCTGAGTATCTTCTCTGTGGCCCTGGATA 1 140 0 CTTCTCTGTG 0.722605 -130 CACAGAGAAGATACTCAGAGCCGCAGGACT 1 150 1 ATACTCAGAG 0.6125 -120 TCCTGTCCTGCTTATCTGAATCTCTGCCTC 1 247 0 CTTATCTGAA 0.947405 -23 TAGGGATTAACTCATCAGAGAAAGGATGAT 2 38 1 CTCATCAGAG 0.958163 -23 AATAAAGTTTCTCATCTTAAATGTTTAAGT 4 26 0 CTCATCTTAA 0.936418 -85 ATAAATGTCTCTTCCCTTAATAAAGTTTCT 4 44 0 CTTCCCTTAA 0.620292 -67 GATTACACCTCATCAGCGTCAGGAAAAA 4 93 0 CTCATCAGCG 0.773185 -18 ATAATTTATTATAATCTGAGTTCTGAATAA 6 147 1 ATAATCTGAG 0.865872 -83 CATCGTGGTTCTTATCTTAGCTTTGCCTTC 6 206 0 CTTATCTTAG 0.871023 -24 CGCACAGGAACTCCTCTAAACTATTTTTGG 7 54 1 CTCCTCTAAA 0.815398 -93 GTCCCTCCTCTGAAATTCGGCGAG 7 133 0 CTCCTCTGAA 0.983968 -14 TACGGACGTTCTAATCTGAGGGTGATGTAT 9 76 0 CTAATCTGAG 0.930581 -114 GTGATGGTTCATCACCTGAGCTTGACTTTA 9 115 1 ATCACCTGAG 0.919332 -75 GTTATGGTTCATCACCTTAACTATTGACTG 9 151 1 ATCACCTTAA 0.627887 -39 GCTGACTCATATGAAAAACTTCAGA 11 91 0 CTCATATGAA 0.710947 -15 ********** Masking position 2 Map Score: 13.8391 Number of sites scoring better than the average of aligned sites = 1135 Number in coding regions = 1054 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 GCTGACAACTATTAATAGTCAGGGAACATAACT 1 52 1 ATTAATATAG 0.832415 -218 AGATAACCATAATATCAGTTATGTTCCCTGACT 1 68 0 AATATCATAG 0.850149 -202 AGTAATAAGTAATATTATTTAAACTTTTCGTAT 3 18 1 AATATTATAA 0.925016 -177 ATTAATAATGATTATTAATGATAAATGTCTCTT 4 61 0 ATTATTATAA 0.944391 -50 AGCGTCAGGAAAAATTAATAATGATTATTAATG 4 74 0 AAAATTATAG 0.880553 -37 GAACACCCTGATAATTTATTATAATCTGAGTTC 6 137 1 ATAATTTTAA 0.588284 -93 AATCAAGAATAATATTATTCAGAACTCAGATTA 6 158 0 AATATTATAA 0.925016 -72 CAGAATTTAAATAATTAATCAAGAATAATATTA 6 174 0 ATAATTATAG 0.910302 -56 ATCTGTCATTATTATTAATGACATATTTCCTAT 8 32 0 ATTATTATAA 0.944391 -33 CATGAATTAAAAAAATATTAACAGAAGGGGG 10 9 0 AAAAATATAA 0.761105 -55 TGTTTAAAAGATTATCAGTTAAAATCACAAACC 11 21 1 ATTATCATAA 0.9047 -85 ATATGTGTTGATAAACAATTAAAATTCAGTTCA 11 57 1 ATAAACATAA 0.710296 -49 ******* * * * Masking position 4 Map Score: 7.30303 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 24 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 CTGAGAAAAAGAACCACGAATACACCCATG 1 18 0 GAACCACGAA 0.984817 -252 CAGAAGGACCGAACCACAGCATGACTCTTC 1 199 0 GAACCACAGC 0.90969 -71 GTAAACCATGAAATGGAGAATC 6 3 1 AAACCATGAA 0.941123 -227 GCTAAGATAAGAACCACGATGGAAG 6 215 1 GAACCACGAT 0.951725 -15 CTCAGGTGATGAACCATCACCCGGTCCTCT 9 105 0 GAACCATCAC 0.933444 -85 TTAAGGTGATGAACCATAACCGAGAATAAA 9 141 0 GAACCATAAC 0.959855 -49 CCAACTATTTAAATCATGAATTAAAAAAAT 10 26 0 AAATCATGAA 0.785226 -38 TTATCAGTTAAAATCACAAACCTTAATATG 11 32 1 AAATCACAAA 0.73738 -74 ********** Masking position 6 Map Score: 3.06306 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 148 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 ATCCCGTGCAGTCTCTCCCTTGCAAGACAT 1 111 0 GTCTCTCCCT 0.983847 -159 CTTCATCAAGGACTCTGTATTCCAGTCCTG 1 173 0 GACTCTGTAT 0.789222 -97 ACCACAGCATGACTCTTCATCAAGGACTCT 1 187 0 GACTCTTCAT 0.960458 -83 GCTTATCTGAATCTCTGCCTCTTCAAGGAA 1 238 0 ATCTCTGCCT 0.923039 -32 TTTTCATCTCTCCATGTTCGAGGAT 3 180 0 ATCTCTCCAT 0.859245 -15 AATGATAAATGTCTCTTCCCTTAATAAAGT 4 48 0 GTCTCTTCCC 0.9005 -63 CCACACAGGGGACACCGCCTGG 5 16 1 GACACCGCCT 0.852557 -12 AGATACCTGAGATTCTCCATTTCATGGTTT 6 13 0 GATTCTCCAT 0.789222 -217 GCCGAGCAGAGACTCCTCCTCAAGGCCGCA 7 28 1 GACTCCTCCT 0.958893 -119 ********** Masking position 5 Map Score: 4.07991 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 410 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 TATCAGTTATGTTCCCTGACTATTAATAGT 1 59 0 GTTCCCTGAC 0.862623 -211 CGTGCAGTCTCTCCCTTGCAAGACATCCTC 1 107 0 CTCCCTTGCA 0.716971 -163 TCTTCTCTGTGGCCCTGGATATCCCGTGCA 1 131 0 GGCCCTGGAT 0.873324 -139 TGAGGACAGGGTTCCTTGAAGAGGCAGAGA 1 227 1 GTTCCTTGAA 0.946671 -43 CACTTCTGGAGGTCCCGGCATTCCTCATAG 2 11 1 GGTCCCGGCA 0.972975 -50 ACTGATAAAAGATCCTGGAGTAGACAGTGA 3 144 1 GATCCTGGAG 0.775328 -51 AGTGAATGCAGATCCTCGAACATGGAGAGA 3 169 1 GATCCTCGAA 0.88532 -26 GATTTACATAGGCCCCGGAAAACCTGAAAA 6 43 1 GGCCCCGGAA 0.972873 -187 TTATCAGGGTGTTCCCTTCACCAGAGGTTT 6 121 0 GTTCCCTTCA 0.788781 -109 GTCTCTGCTCGGCCCTTGCAACCGTCTTCC 7 11 0 GGCCCTTGCA 0.979077 -136 TCCTCGGGTAGACCCTTTCATCCATTTTTA 7 87 0 GACCCTTTCA 0.801525 -60 ACCATCACCCGGTCCTCTACGGACGTTCTA 9 93 0 GGTCCTCTAC 0.652129 -97 ********** Masking position 5 Map Score: 5.37437 Number of sites scoring better than the average of aligned sites = 2728 Number in coding regions = 2638 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 8 ATTCGTGGTTCTTTTTCTCAGGGCTGCTGACA 1 27 1 CTTTTTCTGG 0.918529 -243 TTATGGTTATCTACTTCAGAGGATGTCTTGCA 1 89 1 CTACTTCAGG 0.866909 -181 CAGCATGACTCTTCATCAAGGACTCTGTATTC 1 181 0 CTTCATCAGA 0.866909 -89 AGATGAGAAACTTTATTAAGGGAAGAGACATT 4 39 1 CTTTATTAGG 0.931559 -72 ATATACACATCTTTACCCCGGGACTGACAGGG 6 78 1 CTTTACCCGG 0.976016 -152 AGGGTGTTCCCTTCACCAGAGGTTTTCAGCAA 6 114 0 CTTCACCAGG 0.970601 -116 AGTTCAAGTACTTTTTCCTCGGGTAGACCCTT 7 100 0 CTTTTTCCGG 0.978164 -47 CTGAGCTTGACTTTATTCTCGGTTATGGTTCA 9 130 1 CTTTATTCGG 0.942651 -60 ******** ** Masking position 2 Map Score: 2.70529 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 226 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 AAGAACCACGAATACACCCATGGGGGGAA 1 9 0 AATACACCAT 0.958313 -261 TGAAAACCGGAATATACACATCTTTACCCCG 6 67 1 AATATAACAT 0.957715 -163 TTTCCTATAAAATATATACTTTCAAATAA 8 9 0 AATATAACTT 0.87316 -56 TGAAGGCTTAAATCCATACATCACCCTCAGA 9 61 1 AATCCAACAT 0.958313 -129 TCTTTTAAACAATACAGACAT 11 1 0 AATACAACAT 0.98078 -105 ****** **** Masking position 6 Map Score: 0.190573 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 7 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ********** No masking Map Score: 1.23224e-13 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: 1.23224e-13 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: 1.23224e-13 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