AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -imodE_aquae_opreg_100.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dmsB2 232 dimethylsulfoxide reductase chain B #2 kdsA 264 3-deoxy-d-manno-octulosonic acid 8-phosphate synthase #3 mtfB 300 mannosyltransferase B #4 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #5 gltX 279 glutamyl-tRNA synthetase #6 dmsA 23 DMSO reductase chain A #7 oadA 43 oxaloacetate decarboxylase alpha chain #8 acrR2 272 transcriptional regulator (TetR/AcrR family) #9 moaE 45 molybdopterin converting factor subunit 2 Motif number 1 TGAAAGTAAGAAGGATGAGGAGCTGAATGAAG 1 33 0 AAGGGAGGAG 0.982256 -200 TTCCCGAGGTAAGGAGAAGTAAAATTTACTGG 1 86 1 AAGGAAGTAA 0.779224 -147 GATAAGTATTAAGGGGGAAAAGTCAATGCCGT 1 179 0 AAGGGAAAAG 0.917019 -54 TAGAGAGTATAAGGATAAGTATTAAGGGGGAA 1 192 0 AAGGAAGTAT 0.779224 -41 GTATCCTCAGGAGGATAGAGAGTATAAGGATA 1 207 0 GAGGAGAGAG 0.676167 -26 AGAAAACAAGAACGCTGAGGAGGAAAAACCTC 2 137 0 AACGGAGGAG 0.949783 -128 TGTAAAAGTAAACGATAAAGAAAACAAGAACG 2 155 0 AACGAAAGAA 0.836774 -110 TTACTTTTACAAGGCTGAAGGGGCTATTCTCT 2 176 1 AAGGGAAGGG 0.873722 -89 AACGCCCGAGAAGGTGGGAAATCGTAAAGAGA 2 203 0 AAGGGGAAAT 0.596672 -62 TTTTTAGAGTAAGGTTAAATTAGTAGTT 2 247 1 AAGGAAATTA 0.546796 -18 GTGGAAGGAGAAAGTGGTGTATGGCA 3 5 1 AAGGAAAGTG 0.945747 -296 CCATCGCTCGAAGGTTGAAAAGAAGCTCTCAA 3 49 0 AAGGGAAAAG 0.917019 -252 AGAAAATAATCAGGTCAGGGAGATCATAACAG 3 211 1 CAGGAGGGAG 0.693867 -90 CAACCCATAGAAGGGCAAATATTCACCGA 5 8 0 AAGGAAATAT 0.764786 -272 TGTTTACTACAACGTCAAAGTTTTTACAAACC 5 153 1 AACGAAAGTT 0.655123 -127 CCCTGAAGAAAAGGTCAAGGAGCCTGTACTTT 5 189 0 AAGGAAGGAG 0.980768 -91 TTGTAATTCAAAGGTTAAAATAAACTCTC 5 261 1 AAGGAAAATA 0.546796 -19 CACTACGAGGAAGGTAAGGGAAGGCGATAAAG 8 64 0 AAGGAGGGAA 0.872233 -209 AGTTGCCATAAACGAAGAGGTTGTTCCGAAAT 8 103 0 AACGGAGGTT 0.691503 -170 AATAGTCCTGAACGGCGAAGAGAGAGAAATAC 8 202 0 AACGGAAGAG 0.945722 -71 **** ****** Masking position 2 Map Score: 18.8462 Number of sites scoring better than the average of aligned sites = 2515 Number in coding regions = 2368 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 CTGAGTATCCTCAGGAGGATAGAGAGTA 1 215 0 CCTCAGGAGG 0.838565 -18 AAACAAGAACGCTGAGGAGGAAAAACCTCA 2 136 0 GCTGAGGAGG 0.982013 -129 CTTTTACAAGGCTGAAGGGGCTATTCTCTT 2 179 1 GCTGAAGGGG 0.955089 -86 ATGATGATGAGGTCAGGTGGTATGAGAGAT 3 156 1 GGTCAGGTGG 0.98743 -145 ATGAGAGATGGCTGTGGTGGAGTTGATGTG 3 177 1 GCTGTGGTGG 0.956036 -124 AAAATAATCAGGTCAGGGAGATCATAACAG 3 213 1 GGTCAGGGAG 0.968352 -88 ACAAAAACAGGGAGTGGAGGTTCAACCCAT 5 32 0 GGAGTGGAGG 0.90253 -248 TGAAATTGACGGTGAAGCGGAAGAAATAGA 5 80 0 GGTGAAGCGG 0.961617 -200 CTGAAGAAAAGGTCAAGGAGCCTGTACTTT 5 189 0 GGTCAAGGAG 0.883439 -91 TTTTAAAGCTGGTGAGGTGATAGC 7 30 1 GGTGAGGTGA 0.880701 -14 CAGGGAAGTGGGACTGGCAGTTGCCATAAA 8 123 0 GGACTGGCAG 0.674904 -150 ********** Masking position 7 Map Score: 9.99317 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 405 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TAAGTATTAAGGGGGAAAAGTCAATGCCGTTA 1 177 0 GGGGGAAATC 0.953183 -56 AGCCAAAAAAGGGAAAAATCCCATAGTAACCT 2 98 1 GGGAAAAACC 0.976376 -167 AACGCTGAGGAGGAAAAACCTCACGGGAAAGG 2 127 0 AGGAAAAATC 0.94706 -138 GGAAATCGTAAAGAGAATAGCCCCTTCAGCCT 2 187 0 AAGAGAATCC 0.89456 -78 AAAAAGAGCTGGAAGAAACGCCCGAGAAGGTG 2 219 0 GGAAGAAACC 0.858999 -46 GTTTAAAGTTGGGATAATGATCATGATGATGA 3 134 1 GGGATAATTC 0.891356 -167 TGATGTGGACGAGAAAATAATCAGGTCAGGGA 3 200 1 GAGAAAATTC 0.897184 -101 ACCCATAGAAGGGCAAATATTCACCGA 5 6 0 GGGCAAATTC 0.891802 -274 AATTTCAACAAGGAGAATTCCCGTGTCCTGTG 5 103 1 AGGAGAATCC 0.97461 -177 AGAAATACCTAGGGAAATGACCATAATGGAAC 8 178 0 AGGGAAATCC 0.916606 -95 ACGGCGAAGAGAGAGAAATACCTAGGGAAATG 8 191 0 GAGAGAAACC 0.949346 -82 ATTTAATTTTAGGAAAAAACTCGCTACTT 9 8 0 AGGAAAAATC 0.94707 -38 ******** ** Masking position 6 Map Score: 11.5315 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 565 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 GAATGAAGACTTTAACGAGTTTTATTATCA 1 4 0 TTGTTTTTTA 0.908216 -229 CGTTAATCGGTTTTACGACTTTCCTTATCGGCTCTAA 1 145 0 TTGTTTCTTA 0.973171 -88 TATAGGCTTTTTAAGCGGTTTCCTTTACAACGAAAGC 2 50 1 TTGTTCCTTA 0.991045 -215 TCTTGTTTTCTTTATCGTTTACTTTTACAAGGCTGAA 2 158 1 TTGTACTTTA 0.826374 -107 TTGAATTTATAGGTATTCAGTTAAAAATCACCC 3 278 0 TTGTTCATTA 0.96794 -23 ATCATGAACATGGTAAGGCTTCAATTAATATACCCTG 5 216 0 TGGTTCATTA 0.875841 -64 CAACTTCCACTTTATCGCCTTCCCTTACCTTCCTCGT 8 55 1 TTGTTCCTTA 0.991046 -218 CCCCTATCTCTTCCAGGAGTTCCATTATGGTCATTTC 8 160 1 TTGTTCCTTA 0.991045 -113 TAATTTATAAATATAAGAATTTCTTTATTACTTTGGT 8 244 1 ATGTTTCTTA 0.851149 -29 ** * **** *** Masking position 10 Map Score: 7.59318 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 168 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TATCCTTATACTCTCTATCCTCCTGAGGAT 1 207 1 CTCTCTATCC 0.920811 -26 TGCCATACACCACTTTCTCCTTCCAC 3 7 0 CACTTTCTCC 0.931565 -294 ATAGCCCTTTCTATTTCTTCCGCTTCACCG 5 71 1 CTATTTCTTC 0.951179 -209 GATTTCGGAACAACCTCTTCGTTTATGGCA 8 102 1 CAACCTCTTC 0.918696 -171 AACTTAACCCCTATCTCTTCCAGGAGTTCC 8 153 1 CTATCTCTTC 0.982952 -120 CTAGGTATTTCTCTCTCTTCGCCGTTCAGG 8 198 1 CTCTCTCTTC 0.989091 -75 ********** Masking position 6 Map Score: 2.85334 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 217 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GGGTTATAAATTCCATGCTCTGTCCAATAA 3 245 0 TTCCATGCTC 0.970665 -56 TTATCCGATATCATGCTCCTTTGGGACT 4 9 1 TATCATGCTC 0.978022 -55 ATTGAAGCCTTACCATGTTCATGATAAGTT 5 228 1 TACCATGTTC 0.978022 -52 AAAGACGGGCTACCATATTCCTT 6 4 0 TACCATATTC 0.896808 -20 CGCCTTCCCTTACCTTCCTCGTAGTGTACT 8 70 1 TACCTTCCTC 0.903896 -203 ATTTATAAATTATCATGCCCAGAATAGTCC 8 226 0 TATCATGCCC 0.943111 -47 ********** Masking position 6 Map Score: 2.56058 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 46 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TTATCGGCTCTAAAAAGGGAGACACTATCC 1 128 0 TAAAAAGGGA 0.902581 -105 GAAAGCATATACAGAAGAGCCAAAAAAGGG 2 81 1 ACAGAAGAGC 0.773982 -184 CAGAAGAGCCAAAAAAGGGAAAAATCCCAT 2 92 1 AAAAAAGGGA 0.953404 -173 ACCTTACTCTAAAAAAGAGCTGGAAGAAAC 2 232 0 AAAAAAGAGC 0.931169 -33 GGTTCAACCCATAGAAGGGCAAATATTCAC 5 14 0 ATAGAAGGGC 0.891171 -266 ATTTTATACAAAAACAGGGAGTGGAGGTTC 5 39 0 AAAACAGGGA 0.84459 -241 GCGGAAGAAATAGAAAGGGCTATAGATTTT 5 64 0 TAGAAAGGGC 0.903241 -216 GTAGTAAACATAAGGAGGGCACAGGTTTCA 5 133 0 TAAGGAGGGC 0.919982 -147 AAAGACGGGCTACCATATTC 6 14 0 AAAGACGGGC 0.915491 -10 CTGAACGGCGAAGAGAGAGAAATACCTAGG 8 197 0 AAGAGAGAGA 0.548208 -76 ********** Masking position 7 Map Score: 4.20859 Number of sites scoring better than the average of aligned sites = 793 Number in coding regions = 726 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 TACTTCTCCTTACCTCGGGAAACCAAGACC 1 77 0 TACCTCGGGA 0.840985 -156 CGGGAAAGGTTACTATGGGATTTTTCCCTT 2 106 0 TACTATGGGA 0.89382 -159 GATATCATGCTCCTTTGGGACTTGGACTTG 4 17 1 TCCTTTGGGA 0.854057 -47 GAGAGAGAAATACCTAGGGAAATGACCATA 8 185 0 TACCTAGGGA 0.564801 -88 ATTTCTTTATTACTTTGGTAT 8 262 1 TACTTTGGTA 0.878924 -11 ********** Masking position 1 Map Score: 1.38123 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 50 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 AGTGTCTCCCTTTTTAGAGCCGATAAGGAA 1 132 1 TTTTTAGAGC 0.974887 -101 TTCCAGCTCTTTTTTAGAGTAAGGTTAAAT 2 237 1 TTTTTAGAGT 0.961074 -28 ACAGATGGCTTATTGAGAGCTTCTTTTCAA 3 37 1 TATTGAGAGC 0.90727 -264 CGAGCGATGGTTTGGAGAGTATGTAGTGAG 3 71 1 TTTGGAGAGT 0.88215 -230 AATGAGCATGTGTTTAAAGTTGGGATAATG 3 123 1 TGTTTAAAGT 0.789795 -178 ATATTATTAGTTTTTAAAGCTGGTGAGGTG 7 19 1 TTTTTAAAGC 0.9291 -25 ********** Masking position 6 Map Score: 0.298998 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 82 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ********** No masking Map Score: 2.60302e-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 11 ********** No masking Map Score: 2.60302e-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: 2.60302e-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