AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -igalR_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH412 300 conserved protein #2 MTH442 195 excinuclease ABC subunit B #3 MTH443 41 excinuclease ABC subunit A #4 MTH444 133 sensory transduction histidine kinase #5 MTH446 97 sensory transduction regulatory protein #6 MTH447 109 sensory transduction regulatory protein #7 MTH448 74 unknown #8 MTH449 38 unknown #9 MTH451 132 magnesium chelatase subunit ChlI #10 MTH452 45 unknown #11 MTH625 107 unknown #12 MTH626 36 unknown #13 MTH631 143 UDP-glucose 4-epimerase Motif number 1 CCATGAAACGCATGGCTCTTCACGGATCTCT 4 66 1 CTGGCTCTTC 0.973317 -68 CTTCACGGATCTCTGCTCTTCCAGAGGTCCG 4 83 1 CCTGCTCTTC 0.994791 -51 ATTTTTCTGACTCTCCTCTTCTGGTC 4 118 1 CCTCCTCTTC 0.989941 -16 CTTCACTGGTGTCTGGTCTTCAAGACATGC 5 10 0 GCTGGTCTTC 0.972789 -88 AAATTTTATTGTGGGCTCTTCACTGGTGTCT 5 27 0 GGGGCTCTTC 0.929351 -71 TCCGGTTCCTCTTCATTACGGTTA 5 84 0 GTTCCTCTTC 0.959422 -14 GTTTTCATGAAATTCCTCATCTCTGGCGGTT 11 12 1 ATTCCTCATC 0.75738 -96 CTGCTGGCTGCGCTGCTCATCTCACCCTACA 11 52 1 CCTGCTCATC 0.990116 -56 TCACCCTACACCCTGGTCATCAGGGGTACTA 11 73 1 CCTGGTCATC 0.968265 -35 * ********* Masking position 7 Map Score: 10.5989 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 197 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 CATTTAAAATTTTTTGTGTGTCCAGAAAGTGGATCT 1 48 1 TTTTTTGAGA 0.682959 -253 CAGAGAGCTTTTTATTTTTGAGATAAATGGATATGC 1 127 0 TTATTTGTAA 0.881968 -174 CTCATATATGTCTTTTTTTGGGCTGAAAAATCGCAA 1 186 1 TTTTTTGTGA 0.956307 -115 AATCGCAATATTTATATATGATTTGAGATTCAAGTT 1 214 1 TTATTTGTGA 0.966304 -87 TTTATCATTACCATCCTCTGATTTATGTTTA 2 6 1 CTTACTCTGA 0.768121 -190 CCACGTGTTCCATAATCCTGTGATGATACCCCCACT 2 52 0 CTAACTGTGA 0.960447 -144 ACATTTTCTGGTAATGAGAATTAAGGC 3 2 1 CTTTCGGTGA 0.825047 -40 AACTCTTTAATCCTGCCTTAATTCTCATTAC 3 21 0 TTAACTGTAA 0.838099 -21 CATGGAACCTCTTATCCATGAAATGATAAGAGTGGA 4 35 0 CTATCTGTGA 0.97674 -99 TCACATTAAACCTTATTCTGCAGTGACATCAAAGTA 6 24 1 CTTATTGTGA 0.938163 -86 CTGACGTCTCTTTATACTTGCTCTGATACGCTCAAC 7 26 0 TTATCTGTGA 0.972237 -49 TGATTTCATATATTAATCTGAGGTGATGTT 13 5 0 TTTATTGTGA 0.925835 -139 TATGATTCTGTCTATATTTCTGTTAACATGTAAATA 13 105 0 TTATTTCTAA 0.573094 -39 TAGACAGAATCATATCTGTGTGATAAA 13 127 1 CTATTTGTAA 0.900807 -17 * *** * ** *** Masking position 16 Map Score: 10.8575 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 204 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 TGTCTATCAGTCCAGTAGGGGCATTGATCA 1 96 1 TCCAGTAGGG 0.936721 -205 TTAAAACAAGTTCAGTGGGGGTATCATCAC 2 39 1 TTCAGTGGGG 0.994567 -157 TGTTCCATAATCCTGTGATGATACCCCCAC 2 53 0 TCCTGTGATG 0.825657 -143 TCCCTGCATCAGTGAGGTATCTGATCC 4 8 1 ATCAGTGAGG 0.95765 -126 TTGTGGGCTCTTCACTGGTGTCTGGTCTTC 5 20 0 TTCACTGGTG 0.979599 -78 TGGAACCGCTATCACTGAGGACTAATGTCT 6 75 0 ATCACTGAGG 0.920969 -35 TTACCGGGTTTCAGTGTTGAGCGTATCAG 7 10 1 TTCAGTGTTG 0.935126 -65 CTATCACCGGTTCAGTGGTTGGTCTAATCA 9 112 0 TTCAGTGGTT 0.901327 -21 CTCTGGCGGTTCCACTGGGGCTGCTGGCTG 11 32 1 TCCACTGGGG 0.987312 -76 ********** Masking position 6 Map Score: 9.42839 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 319 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 ACTTTCTGGACACACAAAAAATTTTAAATG 1 48 0 CACACAAAAA 0.957565 -253 GATTTTTCAGCCCAAAAAAAGACATATATG 1 188 0 CCCAAAAAAA 0.957565 -113 GAAATATAATCCCACAATAGAATGAGGTTC 2 160 1 CCCACAATAG 0.966199 -36 CAGTGAAGAGCCCACAATAAAATTTCCAGG 5 33 1 CCCACAATAA 0.98737 -65 GCAAAGGCAGACCACAAAGACCTACCCACA 13 56 1 ACCACAAAGA 0.891903 -88 CAAAGACCTACCCACAAAAACAGGCCACCA 13 70 1 CCCACAAAAA 0.993191 -74 ********** Masking position 6 Map Score: 6.02344 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 37 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 5 TCAGTCCAGTAGGGGCATTGATCAAGCATAT 1 102 1 AGGGGCATGA 0.98659 -199 AGTGCCCGGTAGGGTCACTGTGACATTAAAA 1 249 0 AGGGTCATGT 0.973987 -52 AGTGACCCTACCGGGCACTGTGGATTGGAGG 1 261 1 CCGGGCATGT 0.882328 -40 CATGGATAAGAGGTTCCATGAAACGCATGGC 4 51 1 AGGTTCCTGA 0.947514 -83 TCCAGGCTTAAGGTGTCTTGAGCTCATTAAC 5 57 1 AGGTGTCTGA 0.898998 -41 CCTCTTCATTACGGTTAATGAGCTCAAGACA 5 70 0 ACGGTTATGA 0.827577 -28 CTGCAGAATAAGGTTTAATGTGACGCCGTGA 6 16 0 AGGTTTATGT 0.87854 -94 TCAAAGTATCAGGGGCAATGTCCAGACATTA 6 52 1 AGGGGCATGT 0.980487 -58 TCAGTGATAGCGGTTCCATAAAGGAGGTTTA 6 87 1 CGGTTCCTAA 0.635292 -23 GCTATCACCGGTTCAGTGGTTGGTCTAAT 9 114 0 CGGTTCATGG 0.84744 -19 CCTGGTCATCAGGGGTACTAAGAAGGGGCAG 11 84 1 AGGGGTATAA 0.806356 -24 ******* *** Masking position 9 Map Score: 6.7345 Number of sites scoring better than the average of aligned sites = 1352 Number in coding regions = 1302 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 GGATTTCCATCGAATCCCATTTTAAATATAA 1 8 0 CATCCTTTTA 0.964265 -293 CGATGGAAATCCTATCGCCATTTAAAATTTTTTG 1 30 1 CATCCATTTA 0.972327 -271 GATACCCCCACTGAACTTGTTTTAAACATAAATC 2 30 0 CAACTTTTTA 0.968548 -166 AGACTCCAGACTCAACTTTATGTATCCTGGCAAA 2 106 1 CAACTATGTA 0.925035 -90 ATTAGTAATACTCATCTTTTTTTAGAAATTATTA 9 73 1 CATCTTTTTA 0.97567 -60 AGTGGTTGGTCTAATCATTATTTAATAATTTCTA 9 95 0 CATCTATTTA 0.981145 -38 AAACAGGCCACCAAACCTTATTTACATGTTAACA 13 87 1 CAACTATTTA 0.975668 -57 * *** * ***** Masking position 4 Map Score: 4.85434 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 5 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 GGTATCATCACAGGATTATGGAACACGTGGG 2 58 1 CAGGTTATGG 0.97805 -138 AGAATTAAGGCAGGATTAAAGAGTT 3 27 1 CAGGTTAAAG 0.971917 -15 ATAAAATTTCCAGGCTTAAGGTGTCTTGAGC 5 49 1 CAGGTTAAGG 0.994494 -49 ACTGCAGAATAAGGTTTAATGTGACGCCGTG 6 17 0 AAGGTTAATG 0.842623 -93 AAAGAGACGTCAGGCTGAAGTTATGATGGTA 7 49 1 CAGGTGAAGT 0.958616 -26 CCCTGATGACCAGGGTGTAGGGTGAGATGAG 11 67 0 CAGGTGTAGG 0.973643 -41 **** ****** Masking position 6 Map Score: 3.39574 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 248 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 GCCCAAAAAAAGACATATATGAGCTTTTTAAAT 1 176 0 AGAAATATAG 0.947419 -125 AAAAATCGCAATATTTATATATGATTTGAGATT 1 211 1 ATATATATTG 0.763472 -90 TTGAGTCTGGAGTCTCATATCTGACAGGGTATC 2 88 0 AGTTATATTG 0.897809 -108 ATCCTGGCAAAGGTATATATAAGTTGACCCTGA 2 129 1 AGGAATATAG 0.956061 -67 TAATACAGTCAGGTACATATTAGTAATACTCAT 9 55 1 AGGAATATAG 0.956061 -78 ACCAGGGTGTAGGGTGAGATGAGCAGCGCAGCC 11 57 0 AGGTAGATAG 0.90264 -51 ACATCACCTCAGATTAATATATGAAATCAGACC 13 12 1 AGATATATTG 0.966561 -132 AAATATAGACAGAATCATATCTGTGTGATAAA 13 122 1 AGATATATTG 0.966561 -22 *** * **** ** Masking position 7 Map Score: 4.27124 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 43 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AAATGGCGATAGGATTTCCATCGAATCCCA 1 23 0 AGGATTTCCA 0.933995 -278 GCATTGATCAAGCATATCCATTTATCTCAA 1 116 1 AGCATATCCA 0.919131 -185 CATATCTGACAGGGTATCCCACGTGTTCCA 2 76 0 AGGGTATCCC 0.887799 -120 TTCATGGATAAGAGGTTCCATGAAACGCAT 4 49 1 AGAGGTTCCA 0.961676 -85 CCTCAGTGATAGCGGTTCCATAAAGGAGGT 6 85 1 AGCGGTTCCA 0.990069 -25 CCTCATCTCTGGCGGTTCCACTGGGGCTGC 11 26 1 GGCGGTTCCA 0.973298 -82 ********** Masking position 7 Map Score: 2.24777 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 107 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 GCTCTCTGACGGTCTATTTTAATTTAAAAA 1 155 1 GGTCTATTTT 0.945373 -146 ATAATAAAGGGGTCTGTCCTGTATATAACC 9 19 0 GGTCTGTCCT 0.977737 -114 TAGCTTTAATGGTCTGATTTCATATATTAA 13 25 0 GGTCTGATTT 0.972784 -119 AGGTCTTTGTGGTCTGCCTTTGCATAGCTT 13 49 0 GGTCTGCCTT 0.982814 -95 AAGGTTTGGTGGCCTGTTTTTGTGGGTAGG 13 76 0 GGCCTGTTTT 0.97601 -68 ********** Masking position 5 Map Score: 1.7697 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 49 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 CTATCAGTCCAGTAGGGGCATTGATCAAGC 1 99 1 AGTAGGGGCA 0.988854 -202 CACAGTGCCCGGTAGGGTCACTGTGACATT 1 253 0 GGTAGGGTCA 0.931057 -48 GGGATTATATTTCAGGGTCAACTTATATAT 2 143 0 TTCAGGGTCA 0.928856 -53 ACATCAAAGTATCAGGGGCAATGTCCAGAC 6 49 1 ATCAGGGGCA 0.992195 -61 CACCCTGGTCATCAGGGGTACTAAGAAGGG 11 81 1 ATCAGGGGTA 0.951613 -27 AGGGGTACTAAGAAGGGGCAGAAC 11 94 1 AGAAGGGGCA 0.98051 -14 ********** Masking position 4 Map Score: 4.99747 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 162 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 AATAAAAAGCTCTCTGACGGTCTATTTTAAT 1 147 1 TCTCTGACGT 0.973515 -154 ACAGTGACCCTACCGGGCACTGTGGATTGGA 1 259 1 TACCGGGCCT 0.820263 -42 TGGAGTCTCATATCTGACAGGGTATCCCACG 2 83 0 TATCTGACGG 0.918889 -113 CCGGCTGATTTTTCTGACTCTCCTCTTCTGG 4 111 1 TTTCTGACCT 0.897183 -23 CTGGACATTGCCCCTGATACTTTGATGTCAC 6 46 0 CCCCTGATCT 0.752307 -64 CAAAGAGCGTCCTCTGGCCCG 8 1 0 CCTCTGGCCG 0.938058 -38 TACTAATATGTACCTGACTGTATTAAAAGTA 9 49 0 TACCTGACGT 0.950293 -84 AAATTCCTCATCTCTGGCGGTTCCACTGGGG 11 21 1 TCTCTGGCGT 0.968075 -87 CTGCGCTGCTCATCTCACCCTACACCCTGGT 11 59 1 CATCTCACCT 0.774814 -49 ******** ** Masking position 4 Map Score: 0.877073 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 539 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 ********** No masking Map Score: -1.63892e-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 14 ********** No masking Map Score: -1.63892e-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: -1.63892e-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