AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_mthe_reg_300.orf -o00510_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 Purged sequences: MTH375 26 UDP-glucose 4-epimerase related protein Input sequences: #1 MTH331 208 mannosyltransferase #2 MTH332 119 LPS biosynthesis RfbU related protein #3 MTH338 190 LPS biosynthesis RfbU related protein #4 MTH343 48 rhamnosyl transferase #5 MTH347 60 O-antigen transporter #6 MTH348 194 rhamnosyl transferase #7 MTH370 61 LPS biosynthesis RfbU related protein #8 MTH371 82 unknown #9 MTH372 62 unknown #10 MTH373 142 dTDP-glucose 4,6-dehydratase related protein #11 MTH376 27 conserved protein #12 MTH442 195 excinuclease ABC subunit B #13 MTH443 41 excinuclease ABC subunit A #14 MTH444 133 sensory transduction histidine kinase #15 MTH446 97 sensory transduction regulatory protein #16 MTH447 109 sensory transduction regulatory protein #17 MTH448 74 unknown #18 MTH449 38 unknown #19 MTH1741 86 conserved protein #20 MTH1742 226 conserved protein #21 MTH1745 26 protein disulphide isomerase Motif number 1 AGCTGAACATTTATTACATATTGATGAGGTTTTTATGTAGGA 1 81 1 TTTACATGTT 0.818118 -128 GACATTCTACTTTTAACAGTTAAATGAACCTCTCTTAAATAT 1 126 0 TTTACATGCC 0.886317 -83 TTTTTAGCAGTCTTTACCCCCCACTCGCATTTTGAGGGGCTA 3 61 1 TCTACCTCTT 0.970144 -130 TCATGTCCTCTTTTTACTAGGTGCTCGGCCTCAATCTGAGCA 3 110 0 TTTACCTCCC 0.962255 -81 GGACTTGTAGTTATTACGAAAACCTCATGTCCTCTTTTTACT 3 134 0 TTTACCTCTC 0.978541 -57 GGCATCATCTCCTCACGCTTAACTCCCTTGCATGTGAAGAC 4 18 0 TCTACCTCTC 0.990171 -31 TTTATCATTACCATCCTCTGATTTATGTTTAAAACA 12 5 1 TCTACCTGTT 0.978268 -191 AGTGGGGGTATCATCACAGGATTATGGAACACGTGGGATACC 12 52 1 TCTACATGCC 0.944251 -144 AACGCATGGCTCTTCACGGATCTCTGCTCTTCCAGAGGTCCG 14 72 1 TCTACCTGTC 0.992886 -62 TATTGTGGGCTCTTCACTGGTGTCTGGTCTTCAAGACATGC 15 10 0 TCTACCTGTC 0.992886 -88 GCGTGTACCATCATAACTTCAGCCTGACGTCTCTTTATACTT 17 43 0 TCTACCTGTT 0.978268 -32 TATTTCCTGTTTATTATGACACCCTCTGATCCCGCATCTGGT 20 140 0 TTTATCTCTC 0.765916 -87 ** * ** *** * * Masking position 6 Map Score: 14.3003 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 156 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 TGAGATACATGAAAATCTCTACGTATATTA 1 40 1 GAAAATCTCT 0.814215 -169 TATCCTACATAAAAACCTCATCAATATGTA 1 95 0 AAAAACCTCA 0.964557 -114 TAACAGTTAAATGAACCTCTCTTAAATATT 1 125 0 ATGAACCTCT 0.866587 -84 CATAATCATGATAAATCTCTGAACACATGA 1 166 0 ATAAATCTCT 0.785365 -43 TCCTTAATGAGAACACCTCACACATAATCA 1 188 0 GAACACCTCA 0.919297 -21 AGAGCCTCTGAAAAACCTTAAGATCATAAT 2 89 1 AAAAACCTTA 0.831477 -31 TAGTTATTACGAAAACCTCATGTCCTCTTT 3 139 0 GAAAACCTCA 0.96117 -52 CTGGACCCATATAAACCTCTGCATAGGTGC 8 22 0 ATAAACCTCT 0.93384 -61 CTACTACCTCAAGCACCTTCCAGAGTACAT 9 36 1 AAGCACCTTC 0.530963 -27 ACCTTCCAGAGTACATCTCAGCA 9 50 1 GTACATCTCA 0.691574 -13 TCAAAAACCTTCTTTTTCTGAT 11 3 1 AAAAACCTTC 0.842402 -25 CACTTAAAATAAGAACCTCATTCTATTGTG 12 172 0 AAGAACCTCA 0.926057 -24 GATAAACCTCCTTTATGGAAC 16 99 0 ATAAACCTCC 0.957244 -11 GCACTGCATGGTAAATCTCCTGTGAATTGT 20 110 0 GTAAATCTCC 0.840736 -117 ********** Masking position 5 Map Score: 12.3808 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 563 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 3 TATTAACAGTACCTGAAGCTGAACATTTATT 1 65 1 ACCTGAAGCG 0.841298 -144 GGATTAACTCATCAGAGAAAGGATGATTGA 5 41 1 ATCAGAGAAG 0.968868 -20 ATGCGATCAGAAAAAGAAGGTTTTTG 11 12 0 ATCAGAAAAG 0.940618 -16 TTAAACATAAATCAGAGGATGGTAATGATAA 12 12 0 ATCAGAGGAG 0.989579 -184 AATTCTCATTACCAGAAAATGT 13 2 0 ACCAGAAAAG 0.96192 -40 GACCAGAAGAGGAGAGTCAGAA 14 122 0 ACCAGAAGAG 0.987192 -12 TGTTGAGCGTATCAGAGCAAGTATAAAGAGA 17 25 1 ATCAGAGCAG 0.948066 -50 CGGGCCAGAGGACGCTCTTTGACT 18 4 1 GCCAGAGGAG 0.969307 -35 CATGCAGTGCACCAGATGCGGGATCAGAGGG 20 130 1 ACCAGATGCG 0.919685 -97 CAGATGCGGGATCAGAGGGTGTCATAATAAA 20 142 1 ATCAGAGGGG 0.961863 -85 ********* * Masking position 6 Map Score: 10.7818 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 269 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 CCTATGAGGAATGCCGGGACCTCCAGAAGT 5 12 0 ATGCCGGGAC 0.941736 -49 TAGGATAGGATGGACTGGACTGGACTGGAC 6 101 1 TGGACTGGAC 0.993345 -94 TGGACTGGACTGGACTGGACTGGACTGGAC 6 111 1 TGGACTGGAC 0.993345 -84 TGGACTGGACTGGACTGGACTGGACTGATA 6 121 1 TGGACTGGAC 0.993345 -74 ATATCATTAATTGGCTGGACCCATATAAAC 8 36 0 TTGGCTGGAC 0.976953 -47 CTGAGGACTAATGTCTGGACATTGCCCCTG 16 61 0 ATGTCTGGAC 0.912818 -49 TTGACTTCAATGTCCTGGAC 18 29 1 TGTCCTGGAC 0.932513 -10 GAAGTTTGTGTTGAAGGGACCCTCATACAA 20 72 1 TTGAAGGGAC 0.85612 -155 ********** Masking position 9 Map Score: 10.0776 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 74 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TTCAGAGGCTCTCTTGAAATCTATTGGCTAAT 2 69 0 CTCTGAATCT 0.912493 -51 ATCTGAGCAACTCCTGTAGCCCCTCAAAATGC 3 87 0 CTCTGTACCC 0.942537 -104 AACTCTTTAATCCTGCCTTAATTC 13 28 0 CTCTTAACCT 0.987233 -14 GAGCTCAAGACACCTTAAGCCTGGAAATTTTA 15 50 0 CACTTAACCT 0.96588 -48 GTGTCTTGAGCTCATTAACCGTAATGAAGAGG 15 69 1 CTCTTAACGT 0.927527 -29 GTCACGGCGTCACATTAAACCTTATTCTGCAG 16 15 1 CACTTAACCT 0.96588 -95 CCAACTCTGTCTCCTAAATCCCC 20 2 0 CTCTAAACCC 0.958398 -225 ACACAAACTTCTCCTGAATCCCCTCAAAGTTT 20 51 0 CTCTGAACCC 0.989192 -176 *** **** *** Masking position 8 Map Score: 6.71999 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 97 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TGTAGGATAAATATTTAAGAGAGGTTCATTTAAC 1 116 1 AATTAAGAGG 0.654561 -93 GTCTGTCTTCACATGCAAGGGAGTTAAGCGTGAG 4 14 1 AATGAAGGGT 0.687012 -35 GTTAATCCCTATGAGGAATGCCGGGACCTCCAGA 5 15 0 AGAGAATGGG 0.928847 -46 TTACTGCTGTAGGTTTAAGGGAGGAATAGGATAG 6 75 1 AGTTAAGGGG 0.968346 -120 TAAGGGAGGAATAGGATAGGATGGACTGGACTGG 6 90 1 AAGGTAGGGG 0.742852 -105 CCAATTAATGATATGCAGTGATGGAAGTTGATTG 8 52 1 AATGAGTGGG 0.914422 -31 TCTGAATCGTATATTGTGGGAAGGAAATCTTTAT 10 101 1 AATTTGGGGG 0.839973 -42 TGTTTAAAACAAGTTCAGTGGGGGTATCATCACA 12 36 1 AGTTAGTGGG 0.914422 -160 TCTGGTAATGAGAATTAAGGCAGGATTAAAGAGT 13 17 1 AAATAAGGGG 0.939652 -25 ATGATTAACAATGAGAAATGGAGGTAAACT 19 7 0 AGAGAATGGG 0.928847 -80 TTGGTCAACTAAAATTAATGGGGGTAACGAA 19 66 1 AAATAATGGG 0.906788 -21 ATTGTTAATGAAGTTGTATGAGGGTCCCTTCAAC 20 81 0 AGTTTATGGG 0.871719 -146 * *** **** ** Masking position 1 Map Score: 4.77292 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 367 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 TGTTAATGAGATACATGAAAATCTCTACGT 1 34 1 ATACATGAAA 0.925112 -175 AATATTTATCCTACATAAAAACCTCATCAA 1 101 0 CTACATAAAA 0.774065 -108 AAGGTATAAACTACAGGAAAGCACCTAAGA 2 34 1 CTACAGGAAA 0.717586 -86 TTCTGGGTGAATCCATGAAAATATGTCTTT 3 34 1 ATCCATGAAA 0.9663 -157 CTTTGCCAGGATACATAAAGTTGAGTCTGG 12 111 0 ATACATAAAG 0.791816 -85 GGAACCTCTTATCCATGAAATGATAAGAGT 14 38 0 ATCCATGAAA 0.9663 -96 GGATAAGAGGTTCCATGAAACGCATGGCTC 14 54 1 TTCCATGAAA 0.916356 -80 AAGAGCAGAGATCCGTGAAGAGCCATGCGT 14 73 0 ATCCGTGAAG 0.868227 -61 GTGATAGCGGTTCCATAAAGGAGGTTTATC 16 90 1 TTCCATAAAG 0.793228 -20 TTCTTGTTGTCTCTATGAAGCAGTCGCTGC 20 199 0 CTCTATGAAG 0.724418 -28 ********** Masking position 8 Map Score: 5.35541 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 304 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 8 TTTCAAGAGAGCCTCTGAAAAACCTTAAGA 2 82 1 GCCTCTGAAA 0.961671 -38 AACTCCTGTAGCCCCTCAAAATGCGAGTGG 3 81 0 GCCCCTCAAA 0.993872 -110 TATATAAGTTGACCCTGAAATATAATCCCA 12 144 1 GACCCTGAAA 0.982079 -52 TCTGGACATTGCCCCTGATACTTTGATGTC 16 48 0 GCCCCTGATA 0.988626 -62 TTCTCCTGAATCCCCTCAAAGTTTGTATCA 20 45 0 TCCCCTCAAA 0.96167 -182 GTGTTGAAGGGACCCTCATACAACTTCATT 20 79 1 GACCCTCATA 0.967074 -148 ********** Masking position 6 Map Score: 6.99686 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 175 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ACCTTAAGATCATAATTACCTTCTCAA 2 103 1 CATAATACCT 0.855993 -17 ATTACGAAAACCTCATGTCCTCTTTTTACTA 3 133 0 CCTCATTCCT 0.808112 -58 GGCATCATCTCCTCACGCTTAAC 4 36 0 CATCATTCCT 0.952816 -13 CAGTCCAGTCCATCCTATCCTATTCCTCCCT 6 92 0 CATCCTTCCT 0.974624 -103 ACAGCACAGACAGCCTCTACTACCTCAAGCA 9 20 1 CAGCCTTACT 0.927365 -43 TATGAGACTCCAGACTCAACTTTATGTATCC 12 102 1 CAGACTAACT 0.789834 -94 TCAGAAAAATCAGCCGGACCTCTGGAAGAGC 14 97 0 CAGCCGACCT 0.92022 -37 GCTGATTTTTCTGACTCTCCTCTTCTGGTC 14 114 1 CTGACTTCCT 0.642409 -20 ATCATAACTTCAGCCTGACGTCTCTTTATAC 17 45 0 CAGCCTACGT 0.888032 -30 GCGTGTACCATCATAACTTCAGCCTGACG 17 56 0 CATCATACTT 0.677057 -19 TTTAGAGGTCATCATGAACTGCAGGA 21 10 1 CATCATAACT 0.855993 -17 ****** **** Masking position 11 Map Score: 3.82193 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 570 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 TAGGATGGACTGGACTGGACTGGACTGGACTG 6 106 1 TGGACTGGAG 0.905857 -89 TGGACTGGACTGGACTGGACTGGACTGATAAA 6 121 1 TGGACTGGAG 0.905857 -74 ACCCATATAAACCTCTGCATAGGTGCTCCAAC 8 16 0 ACCTCTGCAG 0.828875 -67 TGCTGAGATGTACTCTGGAAGGTGCTTGAGGT 9 41 0 TACTCTGGAG 0.985948 -22 AACTAGGATATACTCTGAATCGTATATTGTGG 10 88 1 TACTCTGAAG 0.950353 -55 CATTAAACCTTATTCTGCAGTGACATCAAAGT 16 27 1 TATTCTGCAG 0.847415 -83 TCTTTATACTTGCTCTGATACGCTCAACACTG 17 22 0 TGCTCTGATG 0.776172 -53 TCAAAGAGCGTCCTCTGGCCCG 18 1 0 TCCTCTGGCG 0.907812 -38 CCGCATCTGGTGCACTGCATGGTAAATCTCCT 20 119 0 TGCACTGCAG 0.966723 -108 AAACAGGAAATACTCAGGACAGCTACTCTGCA 20 170 1 TACTCAGGAG 0.899153 -57 TCAGGACAGCTACTCTGCAGCGACTGCTTCAT 20 183 1 TACTCTGCAG 0.982654 -44 ********* * Masking position 5 Map Score: 7.10329 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 292 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 TTTCGTATGATGATGTGGGGTGCGACAGATT 6 43 1 TGATGTGGGT 0.953088 -152 CTGAATCGTATATTGTGGGAAGGAAATCTTT 10 102 1 TATTGTGGGA 0.978308 -41 AACCTCATTCTATTGTGGGATTATATTTCAG 12 158 0 TATTGTGGGT 0.984761 -38 CTGGAAATTTTATTGTGGGCTCTTCACTGGT 15 31 0 TATTGTGGGT 0.984761 -67 CAACTAAAATTAATGGGGGTAACGAA 19 71 1 TAATGGGGGA 0.934117 -16 ********* * Masking position 4 Map Score: 1.6542 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 GGATAAATATTTAAGAGAGGTTCATTTAAC 1 120 1 TTAAGAGAGG 0.91789 -89 TGCTGTAGGTTTAAGGGAGGAATAGGATAG 6 79 1 TTAAGGGAGG 0.97066 -116 TTAAAACAAGTTCAGTGGGGGTATCATCAC 12 39 1 TTCAGTGGGG 0.966037 -157 GTAATGAGAATTAAGGCAGGATTAAAGAGT 13 21 1 TTAAGGCAGG 0.794385 -21 TCCCTGCATCAGTGAGGTATCTGATCC 14 8 1 ATCAGTGAGG 0.953122 -126 CCATGAAATGATAAGAGTGGATCAGATACC 14 26 0 ATAAGAGTGG 0.706992 -108 TTGTGGGCTCTTCACTGGTGTCTGGTCTTC 15 20 0 TTCACTGGTG 0.571686 -78 TGGAACCGCTATCACTGAGGACTAATGTCT 16 75 0 ATCACTGAGG 0.860975 -35 TAGCGGTTCCATAAAGGAGGTTTATC 16 94 1 ATAAAGGAGG 0.685356 -16 TTACCGGGTTTCAGTGTTGAGCGTATCAG 17 10 1 TTCAGTGTTG 0.660427 -65 TCAACTAAAATTAATGGGGGTAACGAA 19 70 1 TTAATGGGGG 0.752918 -17 ********** Masking position 4 Map Score: 1.47382 Number of sites scoring better than the average of aligned sites = 1024 Number in coding regions = 954 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 13 ACATATTTTCATGGATTCACCCAGAAATCA 3 30 0 ATGGATTCAC 0.940593 -161 CTGGCGAGGGATGGATTCGCTTAACAGATT 10 17 1 ATGGATTCGC 0.978529 -126 CATGCGTTTCATGGAACCTCTTATCCATGA 14 50 0 ATGGAACCTC 0.962789 -84 AACCTCCTTTATGGAACCGCTATCACTGAG 16 86 0 ATGGAACCGC 0.985757 -24 ********** Masking position 5 Map Score: 0.0852225 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 14 ********** No masking Map Score: 4.03831e-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: 4.03831e-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