AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iarcA_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 MTH151 75 methyl coenzyme M reductase system, component A2 homolog #2 MTH155 228 rubredoxin #3 MTH184 125 isocitrate dehydrogenase #4 MTH978 95 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase #5 MTH980 74 conserved protein #6 MTH981 21 aminopeptidase P #7 MTH982 104 unknown #8 MTH1386 300 3-isopropylmalate dehydratase, LeuD subunit #9 MTH1502 189 succinate dehydrogenase, flavoprotein subunit #10 MTH1648 110 dihydrolipoamide dehydrogenase #11 MTH1707 300 cobalamin biosynthesis protein M #12 MTH1726 117 citrate synthase I Motif number 1 TAGTTTGGAAGCTGGGGGTTTTTATGATGTC 3 28 0 GCTGGGGTTT 0.978449 -98 ACGTAGCCCTGCTCTGGATTATAGATTCAAA 4 41 0 GCTCGGATTA 0.936196 -55 AGTATTTATAGGGCCGGGTGAAAATATAGAT 8 113 1 GGGCGGGTGA 0.963725 -188 GATAATGATCACTGGGGGTTCTGT 9 4 0 ACTGGGGTTC 0.766813 -186 GACGTTCTAATCTGAGGGTGATGTATGGATT 9 71 0 TCTGGGGTGA 0.942494 -119 CGTCCGTAGAGGACCGGGTGATGGTTCATCA 9 98 1 GGACGGGTGA 0.959081 -92 CTATTAATTTGGAGAGGGTTATTGA 10 5 0 GGAGGGGTTA 0.939016 -106 TTTAATAAATGGTGGGGATGTGCCAGATAGG 11 99 1 GGTGGGATGT 0.891383 -202 TGCCAGATAGGCGGAGGATTATTACCATTAT 11 119 1 GCGGGGATTA 0.877635 -182 TTGCCGGGGGTCTCAGGGTGTATAATGGTAA 11 140 0 TCTCGGGTGT 0.917975 -161 TCATCCCTCCGCTCAGGGTGCGATATTACCA 11 174 1 GCTCGGGTGC 0.983508 -127 ATTCCTCTGCGCACAGGGTTTAGTTCACAAA 12 83 0 GCACGGGTTT 0.9536 -35 **** ****** Masking position 9 Map Score: 11.3878 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 609 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 GCGAAAGCTTTATAGTGTTGAGAGACCCGGC 2 157 0 TTAGTGTTGA 0.795007 -72 ATTTTAAGGCTGTAATGATAAAAATAGTTTG 3 52 0 TTAATGATAA 0.700687 -74 TGTGGTAATTATAAATAATAG 5 1 1 TTGGTAATTA 0.863073 -74 TACACTGGAATGTGGTGTTGAG 5 63 1 TTGGTGTTGA 0.916326 -12 CTCTCTGTCCTCTGGTGATGA 6 11 1 TTGGTGATGA 0.983153 -11 GATTTAAATATATAGTAATAACTTATTAGTT 8 72 0 TTAGTAATAA 0.859104 -229 CTATAAATACTTTGATAATAAGATTTAAATA 8 93 0 TTGATAATAA 0.75737 -208 AAAGTCAAGCTCAGGTGATGAACCATCACCC 9 113 0 TAGGTGATGA 0.960624 -77 AGTCAATAGTTAAGGTGATGAACCATAACCG 9 149 0 TAGGTGATGA 0.960624 -41 TGCCAAACCTTATAATAATGA 9 179 1 TTAATAATGA 0.6389 -11 CAGGGTGTATAATGGTAATAATCCTCCGCCT 11 127 0 ATGGTAATAA 0.628888 -174 TCCCTTATATTGTGGTAATATCGCACCCTGA 11 186 0 TTGGTAATAT 0.628888 -115 ATATAAAGGTTGAAGTGATTATTACTAATCT 11 223 0 TAAGTGATTA 0.66399 -78 AGGTAAAGGTTGAGGTGATAAA 12 2 0 TAGGTGATAA 0.938433 -116 * ********* Masking position 6 Map Score: 10.303 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 301 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 TTTTATAGATAATTTTAAATTTTAGGAGAG 2 194 1 AATTTTAAAT 0.960544 -35 ATAGATTCAAAATTATAAATCAATCAAAGC 4 22 0 AATTATAAAT 0.909149 -74 TGTGGTAATTATAAATAATAGGCGCC 5 7 1 AATTATAAAT 0.909149 -68 AACTCGTCTGAATTTTACATCTATATTTTC 8 132 0 AATTTTACAT 0.906089 -169 TTAAAAACATCATTATAAATCATTAA 11 7 0 CATTATAAAT 0.903407 -294 AAAAATAGTAAATTTTAAATAGTTCTAGGA 12 35 0 AATTTTAAAT 0.960544 -83 ********** Masking position 6 Map Score: 5.53087 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 4 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 TAGTATATATTCATGGAGCCGGTGGCGA 1 58 1 TCTGGAGCGG 0.93203 -18 AAATAATATCTGCAGGACCCGGAGGTCCTTAA 2 20 0 TGAGGACCGG 0.981136 -209 AATGGGCTGCCATAGGAGCAGGGTACCTGCTG 2 105 0 CAAGGAGCGG 0.925773 -124 GAATCTATAATCCAGAGCAGGGCTACGTCTCT 4 44 1 TCAGAGCAGG 0.826774 -52 AAACACCCCGTAAAGGATCAGCCCACAGAGAC 4 70 0 TAAGGATCGC 0.833511 -26 ATGAAATCTGTACTGAACCAGGCACTGAAGAA 7 22 0 TATGAACCGG 0.929865 -83 CCTCCTTATATATAGAACATGGGGTGCCATGA 7 53 0 TAAGAACAGG 0.930832 -52 TCAAAGTATTTATAGGGCCGGGTGAAAATATA 8 109 1 TAAGGGCCGG 0.986428 -192 AGAACGTCCGTAGAGGACCGGGTGATGGTTCA 9 94 1 TAAGGACCGG 0.994119 -96 TTTAAATAGTTCTAGGATAAGGTAAAGGTTGA 12 20 0 TCAGGATAGG 0.899982 -98 ** ****** ** Masking position 5 Map Score: 6.30658 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 521 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 TCTCAACACTATAAAGCTTTCGCAGTGAATTTT 2 165 1 ATAAAGCTTC 0.84572 -64 TAGGAGAGTAATAAAGATATAGC 2 216 1 ATAAAGATAC 0.756835 -13 TGAAGGGTTCATAAAGGTTCCAGCAAGTGGTCC 8 252 0 ATAAAGGTTG 0.97753 -49 GATTTATTCGATAATGATCACTGGGGGTTCTGT 9 11 0 ATAATGATCG 0.796823 -179 TAATGTTTAGATAAAGATCCGTCACATATAAAG 10 55 1 ATAAAGATCC 0.925183 -56 TCCGTCACATATAAAGATTTGTGGGAAACAATG 10 72 1 ATAAAGATTG 0.971257 -39 ACCATTTATTAAAAAGGTCCATGTCTTTATGTG 11 79 0 AAAAAGGTCG 0.908882 -222 TTCATATAATATAAAGGTTGAAGTGATTATTAC 11 229 0 ATAAAGGTTG 0.97753 -72 TTGGAATTAAAAAAAGATTAAGGAGGCGAATAG 11 277 1 AAAAAGATTG 0.903782 -24 CTAGGATAAGGTAAAGGTTGAGGTGATAAA 12 8 0 GTAAAGGTTG 0.90072 -110 ********* * Masking position 8 Map Score: 5.52893 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 70 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 CGCATAAAGTTATTATGTCAGTAAA 1 3 1 CAAAGTTATA 0.944879 -73 AGATTAATCTCAAAAAAATAATATCTGCAGGAC 2 34 0 CAAAAATATA 0.916031 -195 CCCCAGCTTCCAAACTATTTTTATCATTACAGC 3 42 1 CAATATTTTA 0.881703 -84 TAATAGGCGCCAGATAGTTAGTAACAGAGCATG 5 26 1 CAAAGTTATA 0.944929 -49 ATCTTATTATCAAAGTATTTATAGGGCCGGGTG 8 100 1 CAATATTTTA 0.881703 -201 CCTCCTTTAGCAGAATAATTGAAGGGTTCATAA 8 271 0 CAATAATTAA 0.484053 -30 GAAACAATGCCATTGAATTAATACC 10 96 1 CATAATTATA 0.772261 -15 ATATAGATTCCATAAAATTAAAAACATCATTAT 11 21 0 CAAAATTAAA 0.870114 -280 AGCGACAATGCACAAAGTTTATATATAGATTCC 11 43 0 CAAAGTTTTA 0.921025 -258 TAATTAAGTACACAAAAATAGTAAATTTTAAAT 12 45 0 CAAAAATATA 0.916031 -73 ** * ***** ** Masking position 9 Map Score: 3.59097 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 11 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TATTAGAACTATGGTGCTTCTAGTATATAT 1 38 1 ATGGTGCTTC 0.948305 -38 GAATAATTGAAGGGTTCATAAAGGTTCCAG 8 262 0 AGGGTTCATA 0.964011 -39 GGACCGGGTGATGGTTCATCACCTGAGCTT 9 108 1 ATGGTTCATC 0.982428 -82 ATTCTCGGTTATGGTTCATCACCTTAACTA 9 144 1 ATGGTTCATC 0.982428 -46 CGGGGGTCTCAGGGTGTATAATGGTAATAA 11 137 0 AGGGTGTATA 0.847118 -164 ********** Masking position 5 Map Score: 0.751877 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 60 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 TATATTCATGGAGCCGGTGGCGA 1 63 1 GAGCCGGTGG 0.989307 -13 ATATCTGCAGGACCCGGAGGTCCTTAAAAA 2 17 0 GACCCGGAGG 0.968987 -212 AATAGTTTGGAAGCTGGGGGTTTTTATGAT 3 31 0 AAGCTGGGGG 0.934728 -95 AGTATTTATAGGGCCGGGTGAAAATATAGA 8 113 1 GGGCCGGGTG 0.958031 -188 ATGTGCCAGATAGGCGGAGGATTATTACCA 11 116 1 TAGGCGGAGG 0.91382 -185 GGGATGACCATTGCCGGGGGTCTCAGGGTG 11 151 0 TTGCCGGGGG 0.975761 -150 ATCGCACCCTGAGCGGAGGGATGACCATTG 11 168 0 GAGCGGAGGG 0.934926 -133 ********** Masking position 6 Map Score: 1.76577 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 232 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 GGGCTACGTCTCTGTGGGCTGATCCTTTAC 4 63 1 TCTGTGGGCT 0.954161 -33 TTACTAACTATCTGGCGCCTATTATTTATA 5 20 0 TCTGGCGCCT 0.988828 -55 CTCTCTGTCCTCTGGTGATGA 6 4 1 TCTGTCCTCT 0.93353 -18 TGGATAACTGTCTTTCGCCTTCATACTGAA 8 163 0 TCTTTCGCCT 0.974126 -138 TCAATCAGGATCAGTCGCCTGATTTATTCG 9 34 0 TCAGTCGCCT 0.98353 -156 ********** Masking position 1 Map Score: 0.310035 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 = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 GTGCTTCTAGTATATATTCATGGAGCCGGT 1 51 1 TATATATTCA 0.956803 -25 GCTATATCTTTATTACTCTCCT 2 217 0 TATATCTTTA 0.722813 -12 TGCTCTGGATTATAGATTCAAAATTATAAA 4 33 0 TATAGATTCA 0.94832 -63 AAGTTATTACTATATATTTAAATCTTATTA 8 79 1 TATATATTTA 0.872588 -222 ATTTTACATCTATATTTTCACCCGGCCCTA 8 121 0 TATATTTTCA 0.846114 -180 CTGATGTCCCCATATGTTCACTGGATAACT 8 184 0 CATATGTTCA 0.77799 -117 GAGGGTGATGTATGGATTTAAGCCTTCAAT 9 59 0 TATGGATTTA 0.746458 -131 AAAGTTTATATATAGATTCCATAAAATTAA 11 33 0 TATAGATTCC 0.811158 -268 TCCATGTCTTTATGTGTTCAGCGACAATGC 11 65 0 TATGTGTTCA 0.879971 -236 ********** Masking position 7 Map Score: 1.90665 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 74 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 ********** No masking Map Score: 2.63855e-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: 2.63855e-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: 2.63855e-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