AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -imodE_aful_opreg_300.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 AF0094 300 conserved hypothetical protein #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 AF1205 53 pantothenate permease (panF-2) #8 AF1208 165 conserved hypothetical protein #9 AF1210 108 conserved hypothetical protein #10 AF1622 78 leucine responsive regulatory protein (lrp) #11 AF2005 48 molybdopterin-guanine dinucleotide biosynthesis protein A (mobA) #12 AF2150 51 molybdenum cofactor biosynthesis protein (moaC) #13 AF2180 50 conserved hypothetical protein #14 AF2371 170 A. fulgidus predicted coding region AF2371 #15 AF2374 159 A. fulgidus predicted coding region AF2374 #16 AF2377 115 conserved hypothetical protein #17 AF2378 47 conserved hypothetical protein #18 AF2383 33 conserved hypothetical protein #19 AF2384 190 molybdopterin oxidoreductase, molybdopterin binding subunit Motif number 1 TATTTCCAGCCTTTCCAAAACGAGTTTGTAA 1 201 1 CTTCCAAAAC 0.98334 -100 TTTTGATTGCATTTTCAAAACCGATTTTAGG 2 76 1 ATTTCAAAAC 0.672239 -64 CGATTTTAGGCCAACCAAAAACTTTTTAAAT 2 97 1 CCACCAAAAA 0.730773 -43 TAAATTTAGGCTATCCTAAACATAACG 2 123 1 CTACCTAAAC 0.926517 -17 ACATCTACCTTTTCCCTAAAATCTTCGAATA 3 20 0 TTTCCTAAAA 0.920497 -43 TACGGTGTTAATTTCCAAAACCCTTATATTT 4 25 1 ATTCCAAAAC 0.959099 -75 GTAAACATTGTTAGCCAGAAAGGTTCTGGCA 4 65 1 TTACCAGAAA 0.518908 -35 TCCACCTCCTCTTGCCAGAACCTTTCTGGCT 4 77 0 CTTCCAGAAC 0.928238 -23 TCATAAGGTTTTTCCCTAAAATATTAGGAAA 5 16 0 TTTCCTAAAA 0.920497 -43 ACCTTATGACCTTGCCAAAAAGACACTATTT 5 38 1 CTTCCAAAAA 0.976266 -21 TTTCCCAGCTCTTCCCAATACACAATTTCCA 6 157 1 CTTCCAATAC 0.817128 -144 ATTTAAAATTACTCCCAAAACAAATTTTATA 10 36 0 ACTCCAAAAC 0.837136 -43 AAAAATATATCTTACCGAAACCAACTAAGTA 12 12 0 CTTCCGAAAC 0.917484 -40 GAACTCTTTTCCAAAATAAAGGTAAGC 14 154 0 TTTCCAAAAT 0.695035 -17 GACTTTTAGGCTTTTCTAAAAAACGGAGGAT 16 42 0 CTTTCTAAAA 0.71831 -74 AACTTTTCGGATTGCCTAAAAT 17 2 0 ATTCCTAAAA 0.920572 -46 AGCCAGCAATTTATCCTAAAAATAG 18 5 0 TTACCTAAAA 0.777301 -29 TTTATAGGTTATTACCTAAAATTGAGAATAC 19 92 0 ATTCCTAAAA 0.920572 -99 *** ******* Masking position 10 Map Score: 18.0225 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 271 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 ATAAATTTTGTTTTTGTAATTAAAAATTCGAC 1 38 0 TTTTGAATTA 0.649381 -263 GAATTTTAGTTTAATAAATTTTGTTTTTGTAA 1 51 0 TAATAATTTT 0.844448 -250 AATCGAATTTTTAATATATTTTCGAAAACAAA 1 131 1 TAATAATTTT 0.843972 -170 TCATATCGGATATTTAACTTTTGTGAAGTGTC 1 273 0 TTTTACTTTT 0.912089 -28 TACCTAACAGTGTTTATATTTAACATTATAAG 2 34 1 TTTTAATTTA 0.901768 -106 TATGCATTTTTGATTGCATTTTCAAAACCGAT 2 69 1 TATTGATTTT 0.872751 -71 AACCAAAAACTTTTTAAATTTAGGCTATCCTA 2 109 1 TTTTAATTTA 0.901978 -31 CCAAACGCTGTATTTAAATTTAACGGTGTTTT 6 200 1 TTTTAATTTA 0.901706 -101 TCTTAAAAACTCATTAGCTTTAAATTATTTTT 6 275 0 TATTACTTTA 0.826758 -26 CTATTTGTAGTATTTACCTTTTCTTTAACAGA 8 16 1 TTTTACTTTT 0.912088 -150 AAGTATGTTTTCAATATCATTACATATCATTA 8 119 0 TAATACATTA 0.43149 -47 TTTTCTCTCTTAAATACCTTTTTTACCGGTTT 9 26 1 TAATACTTTT 0.77052 -83 AGGATTTAACTTATTATATTTGATTAATCTTC 9 78 0 TATTAATTTG 0.790049 -31 TGTACCAACATATATAAAATTTGTTTTGGGAG 10 24 1 TTATAAATTT 0.727624 -55 GGGGAAATTGTATTTAAAATTACTCCCAAAAC 10 46 0 TTTTAAATTA 0.790724 -33 AGTTAGTTATTTATTACACTTTTCCGAGGTTT 11 15 0 TATTAACTTT 0.640237 -34 TCCGGAAAAATGAATGGATTTTCGGAGAAGCT 14 107 0 TAATGATTTT 0.726459 -64 TTATTTTTATTTTTTAAATTTTAAACAATCCT 16 15 1 TTTTAATTTT 0.943679 -101 AAAAAGAAAATTATTAAATTTGACTGCACTAA 19 26 0 TATTAATTTG 0.790233 -165 AATAATTTTCTTTTTGTCTTTTAAGTGATTAG 19 43 1 TTTTGCTTTT 0.835403 -148 ACCTATAAACTTTTTGCAATTTCCACGTTATT 19 114 1 TTTTGAATTT 0.771592 -77 ATTTCCACGTTATTTATAATTTCATCAGCACC 19 132 1 TTTTAAATTT 0.872973 -59 * **** ***** Masking position 5 Map Score: 17.5974 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 94 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 3 ACATTTAAAGTCGAATTTTTAATTACAAAA 1 29 1 TCGAATTTTT 0.978719 -272 AAAGTCCTCATCGAATTTTAGTTTAATAAA 1 65 0 TCGAATTTTA 0.918969 -236 TCGGAGCCAACCGAATTGTTCAGAAAGTCC 1 88 0 CCGAATTGTT 0.983596 -213 TCGATTAATTCCGAATTGTTCGGAGCCAAC 1 107 0 CCGAATTGTT 0.983596 -194 TCGGAATTAATCGAATTTTTAATATATTTT 1 123 1 TCGAATTTTT 0.978719 -178 AACAGATTTTTCGAATTGTTCAAGCGAAGC 8 42 1 TCGAATTGTT 0.986359 -124 ********** Masking position 5 Map Score: 8.58981 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 CACCACCCCAAACACTGTTACCTAACAGTG 2 16 1 AACACTGTTA 0.980523 -124 GTTAAATATAAACACTGTTAGGTAACAGTG 2 28 0 AACACTGTTA 0.980523 -112 TTTGGAAATTAACACCGTAAAAAAAACGAA 4 14 0 AACACCGTAA 0.955725 -86 TCAAGTAGTAAACATTGTTAGCCAGAAAGG 4 58 1 AACATTGTTA 0.932126 -42 ATCATGTAAAAACACCGTTAAATTTAAATA 6 210 0 AACACCGTTA 0.990474 -91 TAGGCAACTTAACACCGTTCAAAAATAATT 6 255 1 AACACCGTTC 0.985909 -46 TAGGTTCCAGATCATCGTTCTTACATGCAT 14 33 0 ATCATCGTTC 0.798488 -138 ********** Masking position 4 Map Score: 8.37194 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 42 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 CCCATCACCACCCCAAACACTGTTA 2 1 1 CCCCACCCCA 0.967845 -139 GCAATCAACATCTACCTTTTCCCTAAAATCTTCGA 3 23 0 TCTCTTCCCA 0.852165 -40 TTTCCACCTCCTCTTGCCAGAACCTTT 4 83 0 TCCCTCCTTC 0.728321 -17 GGAATCCTGCCACTCTCAGCCTTATAAGCTCAGG 6 10 1 CCACTCCCTA 0.961535 -291 CTCAGGCTTCCCCTTCTCAACCTCACGCCTCTCAT 6 39 1 CCCCTCCCTA 0.993133 -262 GCGACGAGAACCTTCCACTGCGTGAAGGGAGCAAT 6 76 1 CCTCACCGTA 0.661761 -225 GCTGACCTTATCCTTCTTCACCTCGAAACTTCCCA 6 117 1 TCCCTTCCTG 0.887825 -184 CAGTCTCTTTCCCAGCTCTTCCCAATACACAATTT 6 150 1 CCCCTCCCCA 0.99326 -151 ATCAGTATATCCCATCTTGCCTCCAAAATACCACC 7 19 0 CCCCTTCTCA 0.935508 -35 TCGTTTACGTTCCGGCTTACCTTTATTTTGGAAAA 14 140 1 TCCCTTCTTA 0.849777 -31 CACTGCCACCTCTGCCTCTTCCCCGATCGGGGACA 15 34 0 TCTCTCCCCG 0.834089 -126 CCGGGTTGCCCCATACTCATCGTAAGGCTTTCGCC 15 133 0 CCACTCCGTA 0.869879 -27 AACCCTACTTCGCCTTAAAGCATATAA 17 31 0 CCCCTTCCTA 0.982897 -17 *** *** *** * Masking position 6 Map Score: 11.38 Number of sites scoring better than the average of aligned sites = 1116 Number in coding regions = 1067 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 AACATTTGGTTTAGGGGGAATAATTCAAAC 1 234 0 TTAGGGGGAA 0.823514 -67 TTCGAAGATTTTAGGGAAAAGGTAGATGTT 3 22 1 TTAGGGAAAA 0.952952 -41 CCCTAAAATATTAGGAAAAATTG 5 4 0 TTAGGAAAAA 0.901655 -55 TCCTAATATTTTAGGGAAAAACCTTATGAC 5 18 1 TTAGGGAAAA 0.952952 -41 GTCTCCGCTTCGGGGAAATTGTATTTAA 10 61 0 TTCGGGGAAA 0.981022 -18 GGCAAAACCTCGGAAAAGTGTAATAAAT 11 9 1 CTCGGAAAAG 0.846289 -40 TGAATGGATTTTCGGAGAAGCTCTTTCTTT 14 99 0 TTCGGAGAAG 0.95062 -72 ACGTAAACGATTCCGGAAAAATGAATGGAT 14 120 0 TTCCGGAAAA 0.803794 -51 TTACCTTTATTTTGGAAAAGAGTTC 14 156 1 TTTGGAAAAG 0.650439 -15 ATTGTCCCCGATCGGGGAAGAGGCAGAGGT 15 32 1 ATCGGGGAAG 0.856824 -128 TCTCTGCGAGCTCGGGGACACACCATGTCG 15 83 1 CTCGGGGACA 0.773049 -77 CTATTTTTAGGATAAATTGCTGGCTA 18 7 1 TTAGGATAAA 0.655575 -27 ********** Masking position 2 Map Score: 6.275 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 329 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 AAACCAAATGTTAGGGTTTGCGACACTTCACAAA 1 252 1 TTAGGGTCAC 0.927075 -49 AAAACCGATTTTAGGCCAACCAAAAACTTTTTAA 2 92 1 TTAGGCACAA 0.98131 -48 CTTTTTAAATTTAGGCTATCCTAAACATAACG 2 118 1 TTAGGCACAA 0.554936 -22 AATAATCGAATTAGGCAACTTAACACCGTTCAAA 6 244 1 TTAGGCATAC 0.900062 -57 CTCAAGACTTTTAGGCTTTTCTAAAAAACGGAGG 16 44 0 TTAGGCTCAA 0.886315 -72 ATTTTAGGCAATCCGAAAAGTTATATG 17 4 1 TTAGGCACAA 0.929849 -44 CAATAAAGGATTAGTGCAGTCAAATTTAATAATT 19 16 1 TTAGTGACAA 0.843052 -175 ****** * * ** Masking position 3 Map Score: 3.90728 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 11 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 CGATTATTGATTTATTCGACATT 1 4 1 TTATTGATTT 0.853922 -297 AGTTTAATAAATTTTGTTTTTGTAATTAAA 1 46 0 ATTTTGTTTT 0.847543 -255 TATTATAAAATTTTTGTTTTCGAAAATATA 1 145 0 TTTTTGTTTT 0.972425 -156 GCATTATGCATTTTTGATTGCATTTTCAAA 2 65 1 TTTTTGATTG 0.812105 -75 TTTTTCGTTTTTTTTACGGTG 4 2 1 TTTTCGTTTT 0.891768 -98 ATTTTAAACCTTATTGTTTTACTTTAATTG 13 31 1 TTATTGTTTT 0.917654 -20 TTTTTTATTTTTATTTTTTAA 16 2 1 TTTTTATTTT 0.775643 -114 AATAATTTTCTTTTTGTCTTTTAAGTGATT 19 43 1 TTTTTGTCTT 0.891768 -148 ACAGTGTTTTTTTGATTTTATTTAATAA 19 173 0 TTTTTGATTT 0.948715 -18 ********** Masking position 4 Map Score: 6.15094 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 61 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 CTGAATTCAGACTATTTCCAGCCTTTCCAA 1 189 1 ACTATTTCCA 0.93445 -112 AACTTCCCAGTCTCTTTCCCAGCTCTTCCC 6 143 1 TCTCTTTCCC 0.898458 -158 CTCTTTCCCAGCTCTTCCCAATACACAATT 6 154 1 GCTCTTCCCA 0.80164 -147 TTCCCAATACACAATTTCCATGATTTTTCA 6 168 1 ACAATTTCCA 0.93445 -133 AATTTTAAATACAATTTCCCCGAAGCGGAG 10 57 1 ACAATTTCCC 0.957648 -22 GTTATTTATTACACTTTTCCGAGGTTTTGC 11 12 0 ACACTTTTCC 0.891343 -37 GAACTCTTTTCCAAAATAAAGG 14 159 0 ACTCTTTTCC 0.891343 -12 TAAACTTTTTGCAATTTCCACGTTATTTAT 19 119 1 GCAATTTCCA 0.905596 -72 ********** Masking position 5 Map Score: 3.43071 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 174 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 10 ATACGCATGTTAGCTCACTGAATTCAGACTAT 1 172 1 TAGCTCCTAA 0.967004 -129 TAGATGTTGATTGCTGACTAAGTTGGACC 3 44 1 TTGCTGCTAG 0.938043 -19 TGCCAGAACCTTTCTGGCTAACAATGTTTACT 4 64 0 TTTCTGCTAC 0.855452 -36 GGTCATAAGGTTTTTCCCTAAAATATTAGGAA 5 17 0 TTTTTCCTAA 0.777488 -42 AGCTACAGGATTGCTCCCTTCACGCAGTGGAA 6 88 0 TTGCTCCTCA 0.955082 -213 ACGGCAGATTTTTCTCTCTTAAATACCTTTTT 9 17 1 TTTCTCCTAA 0.969033 -92 GCTCTTTCTTTAGCTCACTCAACGGAAATCCT 14 78 0 TAGCTCCTAA 0.967004 -93 TTAGGATAAATTGCTGGCTAAATCTGA 18 17 1 TTGCTGCTAA 0.980055 -17 ****** ** ** Masking position 5 Map Score: 3.04561 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 81 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 ********** No masking Map Score: -2.0013e-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: -2.0013e-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: -2.0013e-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