AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -imodE_aquae_opreg_300.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 rpmJ 60 ribosomal protein L36 #3 secY 44 preprotein translocase SecY #4 kdsA 264 3-deoxy-d-manno-octulosonic acid 8-phosphate synthase #5 mtfB 300 mannosyltransferase B #6 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #7 gltX 279 glutamyl-tRNA synthetase #8 dmsA 23 DMSO reductase chain A #9 oadA 43 oxaloacetate decarboxylase alpha chain #10 acrR2 272 transcriptional regulator (TetR/AcrR family) #11 moaE 45 molybdopterin converting factor subunit 2 Motif number 1 TTCATTCAGCTCCTCATCCTTCTTACTTTCA 1 34 1 TCCTCTCCTT 0.948869 -199 CAGTAAATTTTACTTCTCCTTACCTCGGGAA 1 86 0 TACTTTCCTT 0.793302 -147 CGGCATTGACTTTTCCCCCTTAATACTTATC 1 180 1 TTTTCCCCTT 0.896106 -53 TCCCCCTTAATACTTATCCTTATACTCTCTA 1 193 1 TACTTTCCTT 0.793302 -40 ATCCTTATACTCTCTATCCTCCTGAGGATAC 1 208 1 TCTCTTCCTC 0.690786 -25 ATAACCTAAGTCCTTGCCTTTTTCAACT 2 8 0 TCCTTCCTTT 0.584839 -53 TCTTCTACCTCCGAGAGAACT 3 1 1 TCTTCACCTC 0.901326 -44 TTACTATGGGATTTTTCCCTTTTTTGGCTCT 4 96 0 ATTTTCCCTT 0.817117 -169 CCCGTGAGGTTTTTCCTCCTCAGCGTTCTTG 4 132 1 TTTTCTCCTC 0.770498 -133 GTTCTTGTTTTCTTTATCGTTTACTTTTACA 4 156 1 TCTTTTCGTT 0.88756 -109 CTCTTTACGATTTCCCACCTTCTCGGGCGTT 4 204 1 TTTCCACCTT 0.708468 -61 AACTACTAATTTAACCTTACTCTAAAAA 4 247 0 AATTTACCTT 0.743347 -18 GCCATACACCACTTTCTCCTTCCAC 5 5 0 ACTTTTCCTT 0.930388 -296 TGAGAGCTTCTTTTCAACCTTCGAGCGATGG 5 50 1 TTTTCACCTT 0.904607 -251 TGACCTGATTATTTTCTCGTCCACATCAACT 5 197 0 ATTTTTCGTC 0.357946 -104 TCGGTGAATATTTGCCCTTCTATGGGTTG 7 9 1 TATTTCCCTT 0.829159 -271 GTTTGTAAAAACTTTGACGTTGTAGTAAACA 7 153 0 ACTTTACGTT 0.810768 -127 AAGTACAGGCTCCTTGACCTTTTCTTCAGGG 7 190 1 TCCTTACCTT 0.946555 -90 GAGAGTTTATTTTAACCTTTGAATTACAA 7 261 0 ATTTTACCTT 0.830862 -19 CAATTGAACAACTTCCACTTTATCGCCTTCC 10 47 1 ACTTCACTTT 0.550497 -226 TTTATCGCCTTCCCTTACCTTCCTCGTAGTG 10 65 1 TCCCTACCTT 0.819451 -208 TTTCGGAACAACCTCTTCGTTTATGGCAACT 10 104 1 ACCTCTCGTT 0.763538 -169 TATTTCTCTCTCTTCGCCGTTCAGGACTATT 10 203 1 TCTTCCCGTT 0.882669 -70 ***** ***** Masking position 10 Map Score: 19.8511 Number of sites scoring better than the average of aligned sites = 3939 Number in coding regions = 3681 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 2 TAACGGCATTGACTTTTCCCCCTTAATACTTA 1 177 1 GATTTCCCCC 0.937955 -56 AGGTTACTATGGGATTTTTCCCTTTTTTGGCT 4 98 0 GGTTTTTCCC 0.973176 -167 CCTTTCCCGTGAGGTTTTTCCTCCTCAGCGTT 4 127 1 GATTTTTCCT 0.929992 -138 AGGCTGAAGGGGCTATTCTCTTTACGATTTCC 4 187 1 GGATTCTCTT 0.863003 -78 CACCTTCTCGGGCGTTTCTTCCAGCTCTTTTT 4 219 1 GGTTTCTTCC 0.818953 -46 TCATCATCATGATCATTATCCCAACTTTAAAC 5 134 0 GAATTATCCC 0.859006 -167 TCCCTGACCTGATTATTTTCTCGTCCACATCA 5 200 0 GAATTTTCTC 0.866296 -101 TCGGTGAATATTTGCCCTTCTATGGGT 7 6 1 GAATTTGCCC 0.859559 -274 CACAGGACACGGGAATTCTCCTTGTTGAAATT 7 103 0 GGATTCTCCT 0.966121 -177 GTTCCATTATGGTCATTTCCCTAGGTATTTCT 10 178 1 GGATTTCCCT 0.890843 -95 CATTTCCCTAGGTATTTCTCTCTCTTCGCCGT 10 191 1 GGTTTCTCTC 0.932959 -82 AAGTAGCGAGTTTTTTCCTAAAATTAAAT 11 8 1 GATTTTTCCT 0.929999 -38 ** ******** Masking position 6 Map Score: 10.8545 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 3 AAATTTTACTTCTCCTTACCTCGGGAAACC 1 83 0 TCTCCTTACC 0.778616 -150 TGAGGTTTTTCCTCCTCAGCGTTCTTGTTT 4 136 1 CCTCCTCAGC 0.954856 -129 AAGAGAATAGCCCCTTCAGCCTTGTAAAAG 4 179 0 CCCCTTCAGC 0.95051 -86 ATCTCTCATACCACCTGACCTCATCATCAT 5 156 0 CCACCTGACC 0.983663 -145 CACATCAACTCCACCACAGCCATCTCTCAT 5 177 0 CCACCACAGC 0.8205 -124 ATTTTCTCGTCCACATCAACTCCACCACAG 5 188 0 CCACATCAAC 0.631961 -113 CTGTTATGATCTCCCTGACCTGATTATTTT 5 213 0 CTCCCTGACC 0.97446 -88 TCTATTTCTTCCGCTTCACCGTCAATTTCA 7 80 1 CCGCTTCACC 0.908472 -200 AAAGTACAGGCTCCTTGACCTTTTCTTCAG 7 189 1 CTCCTTGACC 0.904317 -91 GCTATCACCTCACCAGCTTTAAAA 9 30 0 TCACCTCACC 0.966318 -14 CTTTATCGCCTTCCCTTACCTTCCTCGTAG 10 64 1 TTCCCTTACC 0.806141 -209 CCAGTCCCACTTCCCTGAACTTAACCCCTA 10 136 1 TTCCCTGAAC 0.707885 -137 ********** Masking position 8 Map Score: 9.39316 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 476 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 GAGCCGATAAGGAAAGTCGTAAAACCGATTA 1 148 1 GGAAGTCGTA 0.901671 -85 CCACAATAGCGGAATATCTTAGTATAACCTA 2 31 0 GGAAATCTTA 0.773071 -30 GTTCCATTTCTGGAAAGGATAAC 4 3 0 TGGAAGGATA 0.723616 -262 AAAACCTCACGGGAAAGGTTACTATGGGATT 4 114 0 GGGAAGGTTA 0.82801 -151 CCGAGAAGGTGGGAAATCGTAAAGAGAATAG 4 199 0 GGGAATCGTA 0.958706 -66 AATCAGGTCAGGGAGATCATAACAGATTTAT 5 218 1 GGGAATCATA 0.945356 -83 AAGTCCCAAAGGAGCATGATATCGGATAA 6 9 0 GGAGATGATA 0.865739 -55 AAACTTATCATGAACATGGTAAGGCTTCAAT 7 228 0 TGAAATGGTA 0.845035 -52 AAGGAATATGGTAGCCCGTCTTT 8 3 1 GGAAATGGTA 0.964777 -21 TTTAAAGCTGGTGAGGTGATAGC 9 31 1 GTGAGTGATA 0.647294 -13 GGAAGGTAAGGGAAGGCGATAAAGTGGAAGT 10 57 0 GGAAGCGATA 0.738384 -216 GTTAAGTTCAGGGAAGTGGGACTGGCAGTTG 10 130 0 GGGAGTGGGA 0.855021 -143 AGGACTATTCTGGGCATGATAATTTATAAAT 10 225 1 TGGGATGATA 0.704724 -48 **** ****** Masking position 11 Map Score: 6.21032 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 569 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 ACCGAACCTCCACAATAGCGGAA 2 48 0 GAACCTCCAC 0.978772 -13 TCTTCTACCTCCGAGAGAACTTTA 3 5 1 CTACCTCCGA 0.863184 -40 TCCAGAAATGGAACGTCCAGCAATATGTAT 4 20 1 GAACGTCCAG 0.846758 -245 ACACCACTTTCTCCTTCCAC 5 1 0 CTCCTTCCAC 0.83589 -300 TCTATGGGTTGAACCTCCACTCCCTGTTTT 7 29 1 GAACCTCCAC 0.978772 -251 TTATCTACCTCCAAATTGATTTTA 10 5 1 CTACCTCCAA 0.96429 -268 TTGATTTTATCCACCGCCAACCAATTGAAC 10 26 1 CCACCGCCAA 0.885615 -247 ACCAATTGAACAACTTCCACTTTATCGCCT 10 45 1 CAACTTCCAC 0.972201 -228 TCGTTTATGGCAACTGCCAGTCCCACTTCC 10 120 1 CAACTGCCAG 0.899345 -153 ********** Masking position 4 Map Score: 5.53849 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 175 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 GTGGAAGGAGAAAGTGGTGTATGG 5 5 1 AAGGAGAAAG 0.836117 -296 TAACATAAGGAATGAGCATGTGTTTAAAGT 5 113 1 AATGAGCATG 0.976925 -188 AAGTTGGGATAATGATCATGATGATGAGGT 5 139 1 AATGATCATG 0.770955 -162 GATTTATTGGACAGAGCATGGAATTTATAA 5 242 1 ACAGAGCATG 0.836448 -59 CCAAGTCCCAAAGGAGCATGATATCGGATA 6 12 0 AAGGAGCATG 0.991716 -52 CAATTTCAACAAGGAGAATTCCCGTGTCCT 7 102 1 AAGGAGAATT 0.760268 -178 AGAAAAGGTCAAGGAGCCTGTACTTTGTAT 7 185 0 AAGGAGCCTG 0.967487 -95 TAAAACTTATCATGAACATGGTAAGGCTTC 7 231 0 CATGAACATG 0.710316 -49 AAGGAATATGGTAGCCCGTC 8 1 1 AAGGAATATG 0.807596 -23 ********** Masking position 5 Map Score: 4.75649 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 133 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 TGATAATAAAACTCGTTAAAGTCTTC 1 3 1 ATAAAAATCT 0.955883 -230 TTTAGAGCCGATAAGGAAAGTCGTAAAACCGATT 1 144 1 ATAAGAATCT 0.988515 -89 ATATCTTAGTATAACCTAAGTCCTTGCCTTTTTC 2 15 0 ATAACAATCT 0.969766 -46 GGAAATGACCATAATGGAACTCCTGGAAGAGATA 10 164 0 ATAAGAATCT 0.988515 -109 TACCAAAGTAATAAAGAAATTCTTATATTTATAA 10 248 0 ATAAGAATCT 0.988515 -25 **** * ** ** * Masking position 8 Map Score: 2.15417 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 30 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 8 GTATCCTCAGGAGGATAGAGAGTATAAGGA 1 209 0 GAGGATAGAG 0.897267 -24 GTGGAAGGAGAAAGTGGTGTATGGCA 5 7 1 GGAGAAAGTG 0.753914 -294 CGGTGAAGCGGAAGAAATAGAAAGGGCTAT 7 71 0 GAAGAAATAG 0.949881 -209 TAAAGCTGGTGAGGTGATAGC 9 33 1 GAGGTGATAG 0.886823 -11 TGCCATAAACGAAGAGGTTGTTCCGAAATC 10 102 0 GAAGAGGTTG 0.882463 -171 GGAACTCCTGGAAGAGATAGGGGTTAAGTT 10 153 0 GAAGAGATAG 0.982484 -120 CCTGAACGGCGAAGAGAGAGAAATACCTAG 10 198 0 GAAGAGAGAG 0.985451 -75 ********** Masking position 4 Map Score: 2.17073 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 382 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TCCTTATCGGCTCTAAAAAGGGAGACACTAT 1 130 0 CTCTAAAAGG 0.977773 -103 TAAAGGAAACCGCTTAAAAAGCCTATAATAC 4 46 0 CGCTAAAAAG 0.976275 -219 TTTAACCTTACTCTAAAAAAGAGCTGGAAGA 4 235 0 CTCTAAAAAG 0.985659 -30 TGAAAAGAAGCTCTCAATAAGCCATCTGTTG 5 35 0 CTCTAATAAG 0.967487 -266 **** ****** Masking position 6 Map Score: 0.135847 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 18 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 ********** No masking Map Score: 6.84553e-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: 6.84553e-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: 6.84553e-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