AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -inarL_aful_opreg_100.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #2 AF0154 139 conserved hypothetical protein #3 AF0155 62 A. fulgidus predicted coding region AF0155 #4 AF0157 99 molybdopterin oxidoreductase, iron-sulfur binding subunit #5 AF0176 58 molybdopterin oxidoreductase, molybdopterin binding subunit #6 AF0177 300 tungsten formylmethanofuran dehydrogenase, subunit E (fwdE) #7 AF0396 154 A. fulgidus predicted coding region AF0396 #8 AF0400 84 NADH oxidase (noxA-3) #9 AF0422 138 uroporphyrin-III C-methyltransferase (cysG-1) #10 AF0499 300 molybdopterin oxidoreductase, iron-sulfur binding subunit #11 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #12 AF0950 177 carbon monoxide dehydrogenase, iron sulfur subunit (cooF) #13 AF1205 53 pantothenate permease (panF-2) #14 AF1208 165 conserved hypothetical protein #15 AF1241 81 glutamate-1-semialdehyde aminotransferase (hemL) #16 AF1643 50 conserved hypothetical protein #17 AF1644 35 tungsten formylmethanofuran dehydrogenase, subunit F (fwdF) #18 AF1858 145 NADH oxidase (noxA-5) #19 AF1980 36 heme exporter protein C (helC) #20 AF1984 45 iron-dependent repressor (troR) #21 AF2191 300 A. fulgidus predicted coding region AF2191 #22 AF2384 190 molybdopterin oxidoreductase, molybdopterin binding subunit Motif number 1 GCATAATGCTTATAATGTTAAATATAAACACTGTTAG 2 37 0 TAATTAATTA 0.906052 -103 AGGCCAACCAAAAACTTTTTAAATTTAGGCTATCCTA 2 104 1 AAATTTAATA 0.684789 -36 GTTAATTTCCAAAACCCTTATATTTTATCAAGTAGTA 4 31 1 AAATTAATTA 0.953135 -69 ATCATGTAAAAACACCGTTAAATTTAAATACAGCGTT 6 203 0 AAATTAATTA 0.953155 -98 ACGGTGTTTTTACATGATTAAAAATAATCGAATTAGG 6 222 1 TAATTAAATA 0.895942 -79 CACCGTTCAAAAATAATTTAAAGCTAATGAGTTTTTA 6 267 1 AATTTAAGTA 0.665981 -34 TTCTTTAAGATAAAAACTTAAAACTAATTTGCTTTTT 7 62 1 TAATTAAATA 0.895937 -93 AAATTCAAGCTACAAACTTAAAAAGCAAATTAGTTTT 7 81 0 TAATTAAAGA 0.626898 -74 ATGTATAGAGGAAAACTTTAAATATAATGGGGGATAA 10 89 0 GAATTAATTA 0.845257 -212 ACGCACGAGAAAAAAGATTTTATATAACAAACCTAAA 11 20 0 AAATTTATTA 0.7088 -126 GTAAGGTTTAAATACACTTAGAGTTGAAGCCC 12 156 1 AAATTAAGTA 0.937268 -22 GTATGTTTTCAATATCATTACATATCATTATACAATG 14 112 0 AAATTAATTA 0.953155 -54 ATTTAATGGGAAAAAACTTAAATAAAATGA 15 4 0 AAATTAATAA 0.592792 -78 TCTCAGCAAGAAAACATTTAAAACGAATTGGAGAGAG 15 49 1 AAATTAAAGA 0.779939 -33 AGGGTGTTTAAAAGGTTTTAGAGTTGAGCGAATTT 16 26 1 AAGTTAAGTA 0.755148 -25 TGAAAATATTTAGAGCATTATAATTAATCTATCGAAA 18 34 1 TAATTAAATA 0.895942 -112 AAATATTCACAAAAGGTTTATAACTGAAAGATTTTAT 18 80 1 AAATTAAATA 0.947812 -66 AGACAAAAAGAAAATTATTAAATTTGACTGCACTAAT 22 25 0 AAATTAATTA 0.95313 -166 AAATTGAGAATACTGAGTTATATTTAATTGCTAATCA 22 68 0 TATTTAATTA 0.562798 -123 TGGAAATTGCAAAAAGTTTATAGGTTATTACCTAAAA 22 102 0 AAATTAAGTA 0.937268 -89 TTGCGGTGCTGATGAAATTATAAATAACGTGGAAATT 22 131 0 GAGTTAAATA 0.501603 -60 ** * *** ** * * Masking position 9 Map Score: 18.4547 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 34 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 GCTGCATGTTTTTTGGGTAAAAAGATGCCAGG 1 57 1 TTTTGGGAAA 0.946087 -67 ATATAAACACTGTTAGGTAACAGTGTTTGGGG 2 21 0 TGTTAGGAAA 0.942035 -119 TCAAAACCGATTTTAGGCCAACCAAAAACTTT 2 90 1 TTTTAGGCAC 0.92048 -50 TATTCGAAGATTTTAGGGAAAAGGTAGATGTT 3 20 1 TTTTAGGAAA 0.98634 -43 TTCCCTAAAATATTAGGAAAAATTG 5 4 0 TATTAGGAAA 0.923827 -55 TTTCCTAATATTTTAGGGAAAAACCTTATGAC 5 16 1 TTTTAGGAAA 0.98634 -43 AACTTAACATTTTTGGGTAAGCTGAAAATAGC 8 30 1 TTTTGGGAAC 0.959761 -55 GTCCCCCTCTTTTTAGGCAATATATAAGAATT 9 34 1 TTTTAGGAAA 0.985529 -105 TTGCAGATATTTTTAGGTAAGCTTAAACCAGA 9 81 0 TTTTAGGAAC 0.982275 -58 GTATTCTCAATTTTAGGTAATAACCTATAAAC 22 92 1 TTTTAGGAAA 0.983153 -99 ******* ** * Masking position 4 Map Score: 17.4917 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 6 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 AAGGTTCTGGCAAGAGGAGGTGGAAA 4 84 1 CAAGAGGAGG 0.967785 -16 ATAAGCGCTGCAGTCGGGGGTCC 8 72 1 CAGTCGGGGG 0.926771 -13 CTTGCAATTACAGGAGGTGAACGA 9 5 0 CAGGAGGTGA 0.909244 -134 TATTGCCTAAAAAGAGGGGGACTTGCAATT 9 26 0 AAAGAGGGGG 0.950094 -113 TACCTGCAGGCAAGCGTAGGTAAATCTGAA 12 52 1 CAAGCGTAGG 0.807156 -126 TTGCAGGAGGTGGTATTTTGGAG 13 4 1 CAGGAGGTGG 0.972608 -50 ATTTTGGAGGCAAGATGGGATATACTGATA 13 25 1 CAAGATGGGA 0.730804 -29 GTGGGAAATTAAAGCGGTGATTCGCCTCA 21 10 0 AAAGCGGTGA 0.77003 -291 CAGTAAAAAGCATGCGGGGGGCGGGATTCG 21 187 1 CATGCGGGGG 0.973304 -114 CAAATTTTTCCAAGCGGGGGTTGCCGAGCC 21 266 0 CAAGCGGGGG 0.994337 -35 ********** Masking position 2 Map Score: 9.24227 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 229 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 CTGTTAGGTAACAGTGTTTGGGGTGGTGAT 2 14 0 ACAGTGTTTG 0.967987 -126 CTGTTACCTAACAGTGTTTATATTTAACAT 2 30 1 ACAGTGTTTA 0.97823 -110 CGTTTTTTTTACGGTGTTAATTTCCAAAAC 4 16 1 ACGGTGTTAA 0.948136 -84 TTTCTGGCTAACAATGTTTACTACTTGATA 4 56 0 ACAATGTTTA 0.814991 -44 AAATTTAAATACAGCGTTTGGTTTGAAAAA 6 191 0 ACAGCGTTTG 0.876002 -110 TTTAAATTTAACGGTGTTTTTACATGATTA 6 212 1 ACGGTGTTTT 0.961783 -89 TTATTTTTGAACGGTGTTAAGTTGCCTAAT 6 253 0 ACGGTGTTAA 0.948136 -48 AGCTTCGGCAAGGGTGTTTAAAAGGTTTTA 16 16 1 AGGGTGTTTA 0.893681 -35 ACAGTGTTTTTTTGATTTTA 22 181 0 ACAGTGTTTT 0.951333 -10 ********** Masking position 7 Map Score: 8.88604 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 26 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 AATGCAATCAAAAATGCATAATGCTTATAAT 2 58 0 AAAAGCATAA 0.584658 -82 AAAATCTTCGAATATGAAAAAAA 3 3 0 AATAGAAAAA 0.903884 -60 CACCGTAAAAAAAACGAAAAA 4 1 0 AAAAGAAAAA 0.952449 -99 TCCCTAAAATATTAGGAAAAATTG 5 4 0 ATTAGAAAAA 0.602866 -55 CTACAAACTTAAAAAGCAAATTAGTTTTAAG 7 78 0 AAAAGCAAAT 0.85207 -77 CTTAAACCAGAAAGCGCAAATTTCGAAATTC 9 61 0 AAAGGCAAAT 0.688538 -78 GAGCCAAAATATATCGAAAAATGATGATTTT 10 163 0 ATATGAAAAA 0.53479 -138 GAATCGAATAAAAAAGCAAAAGGTTAATATA 10 216 1 AAAAGCAAAA 0.942698 -85 AGCGTAGGTAAATCTGAAAAATCTTCACCAA 12 64 1 AATCGAAAAA 0.783045 -114 TCTGTTAAAGAAAAGGTAAATACTACAAATA 14 17 0 AAAAGTAAAT 0.471201 -149 TCGCTTGAACAATTCGAAAAATCTGTTAAAG 14 38 0 AATTGAAAAA 0.769768 -128 GTTCCCATTTAATGGGAAAAAACTTAAATAA 15 16 0 AATGGAAAAA 0.783045 -66 TAATCTATCGAAACAGAAAAAGAAATATTCA 18 58 1 AAACGAAAAA 0.884892 -88 CTTAAAAGACAAAAAGAAAATTATTAAATTT 22 37 0 AAAAGAAAAT 0.875202 -154 AATAACGTGGAAATTGCAAAAAGTTTATAGG 22 115 0 AAATGCAAAA 0.853992 -76 CTTATTAAATAAAATCAAAAAAACACTGT 22 172 1 AAAACAAAAA 0.610771 -19 **** ****** Masking position 8 Map Score: 7.31175 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 199 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 6 GCATTATGCATTTTTGATTGCATTTTCAAAA 2 65 1 TTTTGATTGC 0.96147 -75 GAAAAGGTAGATGTTGATTGCTGACTAAGTT 3 37 1 ATTTGATTGC 0.950407 -26 ACGTCGGAAAATTTATATTGCAATATTGCCA 7 124 1 ATTATATTGC 0.902712 -31 TTCGAAATTCTTATATATTGCCTAAAAAGAG 9 40 0 TTTATATTGC 0.923559 -99 GTTAAAAAACTTCTCGATTGCAGATATTTTT 9 99 0 TTTCGATTGC 0.93605 -40 TTTTGTTGTTGATTGCGTTCCGTTGA 18 6 1 TTTTGATTGC 0.96147 -140 CGTCCGTTAAATATATATTGCGAGTCTGGAT 20 25 1 ATTATATTGC 0.902712 -21 ** ******** Masking position 7 Map Score: 4.63478 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 25 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CTTTTCCCTAAAATCTTCGAATATGAAAAA 3 13 0 AAATCTTCGA 0.68627 -50 TATCTTAAAGAAAAATTTAAATATCGTCAG 7 44 0 AAAAATTTAA 0.619085 -111 CTTTAAGATAAAAACTTAAAACTAATTTGC 7 64 1 AAAACTTAAA 0.906056 -91 CGACGTACAGAAAAATTCAAGCTACAAACT 7 100 0 AAAAATTCAA 0.834424 -55 GTACGGCTCGAAAACTTAACATTTTTGGGT 8 18 1 AAAACTTAAC 0.859865 -67 GGAAGGTTAAAAAACTTCTCGATTGCAGAT 9 105 0 AAAACTTCTC 0.763674 -34 GAGGACAATTAAATCTTTAATCTCAATTAC 10 25 1 AAATCTTTAA 0.724378 -276 TGTATAGAGGAAAACTTTAAATATAATGGG 10 95 0 AAAACTTTAA 0.868207 -206 ACATAAGCCAAAATCTTATAATAACCATTA 10 122 1 AAATCTTATA 0.48898 -179 GGCTTTTCTGTAAACTTCAAATTCTCTGTC 10 263 0 TAAACTTCAA 0.86017 -38 ATAACAAACCTAAACTTCAAGCG 11 4 0 TAAACTTCAA 0.86017 -142 TGCCTCTCTTTAAAATTCACTTCGTATGCT 11 71 0 TAAAATTCAC 0.491265 -75 TAAATCTGAAAAATCTTCACCAATTCTCAA 12 72 1 AAATCTTCAC 0.838292 -106 TTAATGGGAAAAAACTTAAATAAAATGA 15 9 0 AAAACTTAAA 0.906056 -73 ACAGAAAAAGAAATATTCACAAAAGGTTTA 18 70 1 AAATATTCAC 0.56123 -76 GATGAATATTTAAACTTATAAGAATATTAA 18 120 0 TAAACTTATA 0.419398 -26 GGAAAAACTTAAAGCCTTGTTCA 19 4 1 AAAACTTAAA 0.906056 -33 CCCCGCTTGGAAAAATTTGAGAATTGCTGT 21 277 1 AAAAATTTGA 0.303784 -24 ********** Masking position 6 Map Score: 12.3892 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 253 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 8 CCCATCACCACCCCAAACACTGTT 2 2 1 CCTCACACCC 0.973838 -138 GGAATCCTGCCACTCTCAGCCTTATAAG 6 6 1 CCGCCCTCCA 0.922313 -295 CTTCCCCTTCTCAACCTCACGCCTCTCATCTGC 6 45 1 TCACCCACCC 0.953872 -256 CTGACCTTATCCTTCTTCACCTCGAAACTTCCC 6 118 1 CCTCTCACTC 0.743652 -183 CCTATCCCCTCCGCACTGCTACTGTGCCT 7 7 1 CCTCCCACGC 0.985223 -148 TTTTAACCTTCCCACAACTCCCCCTT 9 123 1 CCACACTCCC 0.865773 -16 ACTCTACATATCAGCCACACCTCGTTTAAACGA 14 72 0 TCGCCCACTC 0.893729 -94 GCTTTAATTTCCCACCTCAATCCAGGTGAGACT 21 25 1 CCACCCAACC 0.870488 -276 GAGACTGTAACAGTCCTCACTCACAGTGACGGC 21 52 1 CATCCCACCA 0.704164 -249 TCTCATGTCACCTGCCACCCAGCCCTGGTCCTG 21 145 0 CCGCCCCCGC 0.973621 -156 GGGTTCGAATCCCGCCCCCCGCATGCTTTTTAC 21 189 0 CCGCCCCCCA 0.948358 -112 ATTTATAATTTCATCAGCACCGCAAAGTTCTTA 22 143 1 TCTCACACGC 0.78475 -48 ** *** *** ** Masking position 8 Map Score: 6.3987 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 962 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 GGATGGTAAACGAAAGGTATAAATGAATCCTT 1 87 1 CGAAGGTTAA 0.778914 -37 GTTATGTTTAGGATAGCCTAAATTTAAAAAGT 2 117 0 GGTAGCCAAA 0.849898 -23 GTGTCTTTTTGGCAAGGTCATAAGGTTTTTCC 5 32 0 GGAAGGTATA 0.761111 -27 AACATTTTTGGGTAAGCTGAAAATAGCAAGCC 8 35 1 GGAAGCTAAA 0.977287 -50 GATATTTTTAGGTAAGCTTAAACCAGAAAGCG 9 76 0 GGAAGCTAAA 0.977273 -63 GGGGAGTTGTGGGAAGGTTAAAAAACTTCTCG 9 114 0 GGAAGGTAAA 0.961649 -25 TATGTATAGAGGAAAACTTTAAATATAATGGG 10 95 0 GGAAACTTAA 0.666551 -206 TTCCTCTATACATAAGCCAAAATCTTATAATA 10 113 1 CAAAGCCAAA 0.596339 -188 TGCGGACTTAGGAGAGCCAAAATATATCGAAA 10 175 0 GGGAGCCAAA 0.893526 -126 GAAGTTTACAGAAAAGCCGTAATCGGAGGAAT 10 275 1 GAAAGCCTAA 0.785185 -26 GTATCCTGACGGTAAGGTTTAAATACACTTAG 12 145 1 GGAAGGTTAA 0.936646 -33 ** ***** *** Masking position 5 Map Score: 4.83751 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 246 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 TTTCCACCTCCTCTTGCCAGA 4 89 0 TTCCACCTCC 0.970754 -11 AAGCTCAGGCTTCCCCTTCTCAACCTCACG 6 36 1 TTCCCCTTCT 0.863375 -265 CCTATCCCCTCCGCACTGCTAC 7 3 1 TATCCCCTCC 0.934907 -152 TCGTTCACCTCCTGTAATTGCA 9 3 1 GTTCACCTCC 0.916211 -136 GTAATTGCAAGTCCCCCTCTTTTTAGGCAA 9 24 1 GTCCCCCTCT 0.965486 -115 GCCTCCAAAATACCACCTCCTGCAA 13 6 0 TACCACCTCC 0.962252 -48 CGAACCCGCGGACCCCTTCGGGACAGGGTC 21 215 1 GACCCCTTCG 0.831249 -86 ********** Masking position 8 Map Score: 1.55133 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 423 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TTACAGGCTGCATGTTTTTTGGGTAAAAAG 1 51 1 CATGTTTTTT 0.854181 -73 ACACAATTTCCATGATTTTTCAAACCAAAC 6 176 1 CATGATTTTT 0.854181 -125 TGCCTAATTCGATTATTTTTAATCATGTAA 6 231 0 GATTATTTTT 0.786018 -70 GCCTCTCACTGACGATATTTAAATTTTTCT 7 36 1 GACGATATTT 0.786669 -119 ACTTATCCCCCATTATATTTAAAGTTTTCC 10 87 1 CATTATATTT 0.843201 -214 ATCGAAAAATGATGATTTTTGACCTCATAA 10 152 0 GATGATTTTT 0.854181 -149 TCATTTTATTTAAGTTTTTTC 15 2 1 CATTTTATTT 0.843207 -80 ATAACTGAAAGATTTTATTTATTAATATTC 18 99 1 GATTTTATTT 0.843207 -47 TTGCAATTTCCACGTTATTTATAATTTCAT 22 127 1 CACGTTATTT 0.786669 -64 GTGTTTTTTTGATTTTATTTAATAAGAACT 22 168 0 GATTTTATTT 0.843207 -23 ********** Masking position 6 Map Score: 5.00438 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 60 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 AGAAGAAAAGGGCTTAAGGAT 1 113 0 GAAGAAAAGG 0.914588 -11 CGAAGATTTTAGGGAAAAGGTAGATGTTGA 3 24 1 AGGGAAAAGG 0.962577 -39 CGAGGTGAAGAAGGATAAGGTCAGCTACAG 6 112 0 AAGGATAAGG 0.945518 -189 TCGAATAAAAAAGCAAAAGGTTAATATAAG 10 219 1 AAGCAAAAGG 0.941621 -82 AAAATCTGTTAAAGAAAAGGTAAATACTAC 14 22 0 AAAGAAAAGG 0.959628 -144 GTTGCCGAGCCAGGAAAAGGCGCAGGGCTT 21 247 0 CAGGAAAAGG 0.969409 -54 ********** Masking position 5 Map Score: 2.02514 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 163 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 ********** No masking Map Score: 6.75969e-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: 6.75969e-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: 6.75969e-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