AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_mthe_reg_100.orf -o00510_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 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 MTH373 142 dTDP-glucose 4,6-dehydratase related protein #8 MTH375 26 UDP-glucose 4-epimerase related protein #9 MTH376 27 conserved protein #10 MTH447 109 sensory transduction regulatory protein #11 MTH448 74 unknown #12 MTH449 38 unknown #13 MTH1742 226 conserved protein #14 MTH1745 26 protein disulphide isomerase Motif number 1 TAATATACGTAGAGATTTTCATGTATCTCATTAAC 1 35 0 AGAGTTCTGA 0.990654 -174 TACATATTGATGAGGTTTTTATGTAGGATAAATAT 1 95 1 TGAGTTTTGA 0.846739 -114 AACAGTTAAATGAACCTCTCTTAAATATTTATCCT 1 119 0 TGAATTCTAA 0.733062 -90 TTTGAATCTTAGGTGCTTTCCTGTAGTTTATACCT 2 35 0 AGGTTTCTGA 0.743235 -85 AAGGTTTTTCAGAGGCTCTCTTGAAATCTATTGGC 2 73 0 AGAGTTCTGA 0.990654 -47 GGCCTCAATCTGAGCAACTCCTGTAGCCCCTCAAA 3 91 0 TGAGATCTGA 0.915501 -100 AAAGAGGACATGAGGTTTTCGTAATAACTACAAGT 3 139 1 TGAGTTCTAT 0.94758 -52 TATACGATTCAGAGTATATCCTAGTTTAACTCAAA 7 79 0 AGAGTTCTAT 0.961368 -64 TTTGTGTTGAAGGGACCCTCATACAACTTCATTAA 13 76 1 AGGGCTCTAA 0.864536 -151 ATGCGGGATCAGAGGGTGTCATAATAAACAGGAAA 13 145 1 AGAGTTCTAT 0.961368 -82 GTAGCTGTCCTGAGTATTTCCTGTTTATTATGACA 13 161 0 TGAGTTCTGT 0.975571 -66 TTTAGAGGTCATCATGAACTGCAGGA 14 4 1 AGAGCTCTGA 0.976009 -23 **** * ** ** * Masking position 9 Map Score: 12.9441 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 292 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 GTTAAAAGTAGAATGTCATGTGTTCAGAGA 1 151 1 GAATGTCATG 0.888782 -58 GGATAGGATGGACTGGACTGGACTGGACTG 6 103 1 GACTGGACTG 0.9778 -92 GACTGGACTGGACTGGACTGGACTGGACTG 6 113 1 GACTGGACTG 0.9778 -82 GACTGGACTGGACTGGACTGGACTGATAAA 6 123 1 GACTGGACTG 0.9778 -72 CTGCAGAATCTACTGATGGAAGGTG 8 6 1 GAATCTACTG 0.926663 -21 GTATCAGGGGCAATGTCCAGACATTAGTCC 10 57 1 CAATGTCCAG 0.844294 -53 TCTTTGACTTCAATGTCCTGGAC 12 26 1 CAATGTCCTG 0.971748 -13 ACTGCATGGTAAATCTCCTGTGAATTGTTA 13 108 0 AAATCTCCTG 0.871353 -119 GCTGCAGAGTAGCTGTCCTGAGTATTTCCT 13 174 0 AGCTGTCCTG 0.869944 -53 ********** Masking position 4 Map Score: 6.75645 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 334 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 ATTAACAGTACCTGAAGCTGAACATTTATTAC 1 66 1 CCTGAAGCAA 0.853839 -143 TAGGTGCTTTCCTGTAGTTTATACCTTTATAA 2 29 0 CCTGTAGTAT 0.881854 -91 CTGAGCAACTCCTGTAGCCCCTCAAAATGCGA 3 85 0 CCTGTAGCCT 0.972161 -106 GTGGTCTGTCTTCACATGCAAGGGAG 4 5 1 TCTGTCTTCA 0.672875 -44 GCAGTAAAAATCTGTCGCACCCCACATCATCA 6 50 0 TCTGTCGCCC 0.812607 -145 TGTTCGAGGATCTGCATTCACTGTCTACTCCA 6 159 0 TCTGCATTCT 0.874298 -36 TAGGATATACTCTGAATCGTATATTGTGGGAA 7 91 1 TCTGAATCAT 0.764128 -52 TAAACCTTATTCTGCAGTGACATCAAAGTATC 10 30 1 TCTGCAGTCA 0.900775 -80 ATAACTTCAGCCTGACGTCTCTTTATACTTGC 11 41 0 CCTGACGTCT 0.918 -34 TTTCACCAACTCTGTCTCCTAAATCCCC 13 7 0 TCTGTCTCAA 0.603181 -220 ACAAACTTCTCCTGAATCCCCTCAAAGTTTGT 13 49 0 CCTGAATCCT 0.918456 -178 GGACAGCTACTCTGCAGCGACTGCTTCATAGA 13 186 1 TCTGCAGCCT 0.970186 -41 TCCTGCAGTTCATGATGACCTCT 14 14 0 CCTGCAGTAT 0.905746 -13 ******** ** Masking position 3 Map Score: 8.64949 Number of sites scoring better than the average of aligned sites = 1145 Number in coding regions = 1074 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 TCCTACATAAAAACCTCATCAATATGTAAT 1 93 0 AAACCTCATC 0.945643 -116 AGCCTCTGAAAAACCTTAAGATCATAATTA 2 91 1 AAACCTTAAG 0.915665 -29 GTTATTACGAAAACCTCATGTCCTCTTTTT 3 137 0 AAACCTCATG 0.983937 -54 TTCCTCCCTTAAACCTACAGCAGTAAAAAT 6 71 0 AAACCTACAG 0.872055 -124 TCAAAAACCTTCTTTTTCTGATCG 9 5 1 AAACCTTCTT 0.957943 -23 GCGTCACATTAAACCTTATTCTGCAGTGAC 10 21 1 AAACCTTATT 0.934896 -89 GATAAACCTCCTTTATGGAACCG 10 97 0 AAACCTCCTT 0.979185 -13 ACTGCATGGTAAATCTCCTGTGAATTGTTA 13 108 0 AAATCTCCTG 0.91561 -119 ********** Masking position 3 Map Score: 7.78359 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 116 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TGTTCACATTCCCTGTTAATGAGATACATGAAA 1 21 1 CCCTGTTATG 0.909219 -188 CATGGATTCACCCAGAAATCAAGTTTTGATTGA 3 18 0 CCCAGAAACG 0.957692 -173 CTGGGTGAATCCATGAAAATATGTCTTTTTAGC 3 36 1 CCATGAAATG 0.909027 -155 CTCCTGTAGCCCCTCAAAATGCGAGTGGGGGGT 3 76 0 CCCTCAAATG 0.991308 -115 TAGGTGCTCGGCCTCAATCTGAGCAACTCCTGT 3 102 0 GCCTCAATTG 0.804532 -89 AGATTTCCTTCCCACAATATACGATTCAGAGTA 7 98 0 CCCACAATTG 0.898313 -45 TGGACATTGCCCCTGATACTTTGATGTCACTGC 10 43 0 CCCTGATATG 0.972304 -67 ATACGCTCAACACTGAAACCCGGTAA 11 4 0 CACTGAAACG 0.876686 -71 CTCCTGAATCCCCTCAAAGTTTGTATCAAGGCC 13 40 0 CCCTCAAATG 0.991084 -187 TATTATGACACCCTCTGATCCCGCATCTGGTGC 13 138 0 CCCTCTGACG 0.857398 -89 ******** * * Masking position 13 Map Score: 6.75049 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 475 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CCTTAATGAGAACACCTCACACATAATCATG 1 186 0 AACACCTCAA 0.921376 -23 ACTACAGGAAAGCACCTAAGATTCAAATTAG 2 43 1 AGCACCTAAA 0.971115 -77 ATTTCAAGAGAGCCTCTGAAAAACCTTAAGA 2 81 1 AGCCTCTGAA 0.933028 -39 CAACTCCTGTAGCCCCTCAAAATGCGAGTGG 3 81 0 AGCCCCTCAA 0.993649 -110 ATTGAGGCCGAGCACCTAGTAAAAAGAGGAC 3 117 1 AGCACCTAGA 0.911854 -74 GTCTGGACATTGCCCCTGATACTTTGATGTC 10 48 0 TGCCCCTGAA 0.957078 -62 CTTCTCCTGAATCCCCTCAAAGTTTGTATCA 13 45 0 ATCCCCTCAA 0.960323 -182 ********* * Masking position 11 Map Score: 4.17031 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 201 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 AGAATGTCATGTGTTCAGAGATTTATCATGA 1 160 1 GTGTCAGAGA 0.935172 -49 GATCTTAAGGTTTTTCAGAGGCTCTCTTGAA 2 83 0 TTTTCAGAGG 0.801384 -37 GGTCCCGGCATTCCTCATAGGGATTAACTCA 5 21 1 TTCTCATAGG 0.899497 -40 TAGGGATTAACTCATCAGAGAAAGGATGATT 5 38 1 CTCTCAGAGA 0.97712 -23 GAATCCATCCCTCGCCAGAGAGAA 7 4 0 CTCCCAGAGA 0.975573 -139 AGTTATTGAACTCGCCATATAAATAGTTTCA 7 46 0 CTCCCATATA 0.603824 -97 CCAGACATTAGTCCTCAGTGATAGCGGTTCC 10 73 1 GTCTCAGTGA 0.805116 -37 CGGGCCAGAGGACGCTCTTTG 12 1 1 CGGCCAGAGG 0.956969 -38 TACCATGCAGTGCACCAGATGCGGGATCAGA 13 127 1 TGCCCAGATG 0.829598 -100 CACCAGATGCGGGATCAGAGGGTGTCATAAT 13 139 1 GGGTCAGAGG 0.947656 -88 CTGCAGCGACTGCTTCATAGAGACAACAAGA 13 197 1 TGCTCATAGA 0.861825 -30 *** ******* Masking position 7 Map Score: 4.43692 Number of sites scoring better than the average of aligned sites = 1015 Number in coding regions = 949 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 TCTCTACGTATATTAACAGTACCTGAAGCT 1 55 1 TATTAACAGT 0.953349 -154 GACATTCTACTTTTAACAGTTAAATGAACC 1 138 0 TTTTAACAGT 0.981001 -71 AAATATGTCTTTTTAGCAGTCTTTACCCCC 3 52 1 TTTTAGCAGT 0.977478 -139 CTCCAGGATCTTTTATCAGTCCAGTCCAGT 6 134 0 TTTTATCAGT 0.966976 -61 ********** Masking position 5 Map Score: 1.84181 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 6 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 CATATTGATGAGGTTTTTATGTAGGATAAAT 1 97 1 AGGTTTTATG 0.79607 -112 TTGAGAAGGTAATTATGATCTTAAGGT 2 103 0 AGGTATTATG 0.956108 -17 TAGTAAAAAGAGGACATGAGGTTTTCGTAAT 3 133 1 AGGAATGAGG 0.954973 -58 GTTAAGCGTGAGGAGATGATGCC 4 36 1 AGGAATGATG 0.987632 -13 TAACTCATCAGAGAAAGGATGATTGA 5 45 1 GAGAAGGATG 0.733118 -16 AGGGAGGAATAGGATAGGATGGACTGGACTG 6 92 1 AGGAAGGATG 0.978363 -103 CGTCAGGCTGAAGTTATGATGGTACACGC 11 56 1 AAGTATGATG 0.948089 -19 TTTAGAGGTCATCATGAACTGCAGGA 14 6 1 AGGTATCATG 0.94821 -21 **** ****** Masking position 9 Map Score: 4.41042 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 368 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 CCTTAATGAGAACACCTCACACATAATCAT 1 187 0 AACACCTCAC 0.969479 -22 TAGCAGTCTTTACCCCCCACTCGCATTTTG 3 65 1 TACCCCCCAC 0.947463 -126 CAACTCCTGTAGCCCCTCAAAATGCGAGTG 3 82 0 AGCCCCTCAA 0.973963 -109 GGCATCATCTCCTCACGCTTAACTCC 4 33 0 ATCTCCTCAC 0.947406 -16 AAAAATCTGTCGCACCCCACATCATCATAC 6 47 0 CGCACCCCAC 0.94832 -148 CTTCTCCTGAATCCCCTCAAAGTTTGTATC 13 46 0 ATCCCCTCAA 0.960291 -181 ********** Masking position 9 Map Score: 1.52933 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 215 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 11 ********** No masking Map Score: 1.67931e-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 12 ********** No masking Map Score: 1.67931e-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 13 ********** No masking Map Score: 1.67931e-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