AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -inarP_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 AF0950 177 carbon monoxide dehydrogenase, iron sulfur subunit (cooF) #11 AF1241 81 glutamate-1-semialdehyde aminotransferase (hemL) #12 AF1643 50 conserved hypothetical protein #13 AF1644 35 tungsten formylmethanofuran dehydrogenase, subunit F (fwdF) #14 AF1858 145 NADH oxidase (noxA-5) #15 AF1980 36 heme exporter protein C (helC) #16 AF1984 45 iron-dependent repressor (troR) #17 AF2191 300 A. fulgidus predicted coding region AF2191 #18 AF2384 190 molybdopterin oxidoreductase, molybdopterin binding subunit Motif number 1 TTTTAAATTTTCGCTCCTTTG 1 2 1 TTTAAATTTT 0.936785 -122 CCTAACAGTGTTTATATTTAACATTATAAG 2 36 1 TTTATATTTA 0.84068 -104 CCAAAAACTTTTTAAATTTAGGCTATCCTA 2 111 1 TTTAAATTTA 0.929712 -29 CGTTATGTTTAGGATAGCCTA 2 129 0 GTTATGTTTA 0.699259 -11 AAACGCTGTATTTAAATTTAACGGTGTTTT 6 202 1 TTTAAATTTA 0.929712 -99 ACTGACGATATTTAAATTTTTCTTTAAGAT 7 43 1 TTTAAATTTT 0.936785 -112 GCAAATTAGTTTTAAGTTTTTATCTTAAAG 7 64 0 TTTAAGTTTT 0.950512 -91 TAATTTGCTTTTTAAGTTTGTAGCTTGAAT 7 86 1 TTTAAGTTTG 0.800221 -69 AATATTGCAATATAAATTTTCCGACGTACA 7 121 0 TATAAATTTT 0.855325 -34 ACCCAAAAATGTTAAGTTTTCGAGCCGTAC 8 18 0 GTTAAGTTTT 0.867188 -67 CGCTTTCTGGTTTAAGCTTACCTAAAAATA 9 76 1 TTTAAGCTTA 0.789731 -63 TTCGATATATATTTTTTTGCATTCA 10 6 1 TATATATTTT 0.702248 -172 TCATTTTATTTAAGTTTTTTCCCATTAA 11 9 1 TTTAAGTTTT 0.950512 -73 TTAATATTCTTATAAGTTTAAATATTCATC 14 120 1 TATAAGTTTA 0.872439 -26 TGAACAAGGCTTTAAGTTTTTCC 15 4 0 TTTAAGTTTT 0.950512 -33 AGACTCGCAATATATATTTAACGGACGCTG 16 22 0 TATATATTTA 0.677557 -24 AGAATACTGAGTTATATTTAATTGCTAATC 18 69 0 GTTATATTTA 0.642084 -122 GGTAATAACCTATAAACTTTTTGCAATTTC 18 107 1 TATAAACTTT 0.564307 -84 ********** Masking position 3 Map Score: 22.1315 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 31 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 GCTGCATGTTTTTTGGGTAAAAAGATGCCAGG 1 57 1 TTTTGGGAAA 0.941081 -67 ATATAAACACTGTTAGGTAACAGTGTTTGGGG 2 21 0 TGTTAGGAAA 0.95873 -119 TCAAAACCGATTTTAGGCCAACCAAAAACTTT 2 90 1 TTTTAGGCAC 0.952133 -50 TATTCGAAGATTTTAGGGAAAAGGTAGATGTT 3 20 1 TTTTAGGAAA 0.990874 -43 TTCCCTAAAATATTAGGAAAAATTG 5 4 0 TATTAGGAAA 0.95315 -55 TTTCCTAATATTTTAGGGAAAAACCTTATGAC 5 16 1 TTTTAGGAAA 0.990874 -43 AACTTAACATTTTTGGGTAAGCTGAAAATAGC 8 30 1 TTTTGGGAAC 0.976155 -55 GTCCCCCTCTTTTTAGGCAATATATAAGAATT 9 34 1 TTTTAGGAAA 0.989478 -105 TTGCAGATATTTTTAGGTAAGCTTAAACCAGA 9 81 0 TTTTAGGAAC 0.989576 -58 GTATTCTCAATTTTAGGTAATAACCTATAAAC 18 92 1 TTTTAGGAAA 0.985409 -99 ******* ** * Masking position 4 Map Score: 20.1777 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 AACACTGTTAGGTAACAGTGTTTGGGGTGGTG 2 16 0 GGTAAGTGTT 0.889321 -124 AATGCATAATGCTTATAATGTTAAATATAAAC 2 45 0 GCTAAATGTT 0.980623 -95 AACCTTTCTGGCTAACAATGTTTACTACTTGA 4 58 0 GCTAAATGTT 0.980623 -42 TTTTTGGCAAGGTCATAAGGTTTTTCCCTAAA 5 27 0 GGTAAAGGTT 0.976604 -32 GGAAGCCTGAGCTTATAAGGCTGAGAGTGGCA 6 18 0 GCTAAAGGCT 0.959309 -283 ATGTTTTCTTGCTGAGAATGTTCCCATTTAAT 11 34 0 GCTAAATGTT 0.980623 -48 TCTCCAATTCGTTTTAAATGTTTTCTTGCTGA 11 51 0 GTTTAATGTT 0.775169 -31 CGGCAAGGGTGTTTAAAAGGTTTTAGAGTTGA 12 21 1 GTTAAAGGTT 0.963698 -30 CAAAGGGTTAAAAGGCTAAGAATAAAG 13 6 1 GGTAAAGGCT 0.947226 -30 ATTGCGTTCCGTTGAAAATATTTAGAGCATTA 14 22 1 GTTAAATATT 0.681605 -124 *** * ****** Masking position 7 Map Score: 10.0686 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 108 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 AAGGTATAAATGAATCCTTAAGCCCTTTTCTTCT 1 100 1 TAATAAGCTT 0.948704 -24 TAGGATAGCCTAAATTTAAAAAGTTTTTGGTTGGCCT 2 104 0 TAATAAATTT 0.950046 -36 TTTACGGTGTTAATTTCCAAAACCCTTATATTTTATC 4 23 1 TATTAAACTT 0.831627 -77 CTCTTTTTAGGCAATATATAAGAATTTCGAAATTTGC 9 40 1 GAATAAGTTT 0.895955 -99 AAAAATATCTGCAATCGAGAAGTTTTTTAACCTTCCC 9 99 1 GAATAAGTTT 0.895955 -40 CAAATCCCCTTGAATGCAAAAAAATATATATCGAA 10 9 0 TAATAAATAT 0.754397 -169 CAAGCGTAGGTAAATCTGAAAAATCTTCACCAATTCT 10 62 1 TAATAAACTT 0.96835 -116 ATGTTCCCATTTAATGGGAAAAAACTTAAATAAAATG 11 12 0 TAATAAACTT 0.968352 -70 AAATTCGCTCAACTCTAAAACCTTTTAAACACCCT 12 26 0 TAACAAATTT 0.720805 -25 TATAAGAATATTAATAAATAAAATCTTTCAGTTATAA 14 97 0 TAATAAACTT 0.968352 -49 GCTCTCGATGAATATTTAAACTTATAAGAATATTA 14 121 0 TAATAAATAT 0.754397 -25 GGAAAAACTTAAAGCCTTGTTCATACAC 15 2 1 GAAAAAACTT 0.677123 -35 ATAAACAGCAATTCTCAAATTTTTCCAAGCGGGG 17 277 0 GAATAAATTT 0.934411 -24 TGAGTTATATTTAATTGCTAATCACTTAAAAGACAAA 18 55 0 TAATAATCTT 0.77993 -136 AAATAACGTGGAAATTGCAAAAAGTTTATAGGTTATT 18 110 0 GAATAAATTT 0.934411 -81 TTTTTTGATTTTATTTAATAAGAACTTTGCGGTGCTG 18 157 0 TATTAAGCTT 0.74909 -34 * *** *** *** Masking position 10 Map Score: 14.899 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 77 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 TTTCCACCTCCTCTTGCCAGAACCTT 4 84 0 CCTCCTCTTG 0.968757 -16 CCTATCCCCTCCGCACTGCTACTGTGC 7 8 1 CCTCCGCACT 0.882948 -147 GGACCCCCGACTGCAGCGCTTAT 8 72 0 CCCCCGACTG 0.95217 -13 AATTGCAAGTCCCCCTCTTTTTAGGCAATA 9 26 1 CCCCCTCTTT 0.950557 -113 TTCAGATTTACCTACGCTTGCCTGCAGGTA 10 52 0 CCTACGCTTG 0.946167 -126 CGAATCCCGCCCCCCGCATGCTTTTTACTG 17 187 0 CCCCCGCATG 0.99135 -114 GGTCTTAAGCCCTGCGCCTTTTCCTGGCTC 17 241 1 CCTGCGCCTT 0.894113 -60 GGCTCGGCAACCCCCGCTTGGAAAAATTTG 17 266 1 CCCCCGCTTG 0.995368 -35 ********** Masking position 5 Map Score: 7.50439 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 142 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TTTCCACCTCCTCTTGCCAGAACCTTTCTG 4 80 0 CTCTTGCCAG 0.889449 -20 AAACCTTATGACCTTGCCAAAAAGACACTA 5 36 1 ACCTTGCCAA 0.821776 -23 GGAATCCTGCCACTCTCAGCCTT 6 4 1 ATCCTGCCAC 0.94733 -297 CTGCGACGAGAACCTTCCACTGCGTGAAGG 6 74 1 AACCTTCCAC 0.877802 -227 TTCACCTCGAAACTTCCCAGTCTCTTTCCC 6 133 1 AACTTCCCAG 0.926445 -168 TCTTTCCCAGCTCTTCCCAATACACAATTT 6 155 1 CTCTTCCCAA 0.838745 -146 TTATATTGCAATATTGCCACTTGCTCACA 7 136 1 ATATTGCCAC 0.832118 -19 TTTCGAGCCGTACTTCCCAC 8 1 0 TACTTCCCAC 0.89408 -84 AAGTTTTTTAACCTTCCCACAACTCCCCCT 9 118 1 ACCTTCCCAC 0.963863 -21 TCACCGCTTTAATTTCCCACCTCAATCCAG 17 20 1 AATTTCCCAC 0.804505 -281 AGTCTCATGTCACCTGCCACCCAGCCCTGG 17 150 0 CACCTGCCAC 0.960978 -151 AAACTTTTTGCAATTTCCACGTTATTTATA 18 120 1 CAATTTCCAC 0.649282 -71 ********** Masking position 9 Map Score: 7.19084 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 327 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 CTGTTAGGTAACAGTGTTTGGGGTGGTGAT 2 14 0 ACAGTGTTTG 0.92189 -126 CTGTTACCTAACAGTGTTTATATTTAACAT 2 30 1 ACAGTGTTTA 0.974592 -110 CGTTTTTTTTACGGTGTTAATTTCCAAAAC 4 16 1 ACGGTGTTAA 0.975328 -84 TTTCTGGCTAACAATGTTTACTACTTGATA 4 56 0 ACAATGTTTA 0.78993 -44 TTTAAATTTAACGGTGTTTTTACATGATTA 6 212 1 ACGGTGTTTT 0.965021 -89 TTATTTTTGAACGGTGTTAAGTTGCCTAAT 6 253 0 ACGGTGTTAA 0.975328 -48 AGCTTCGGCAAGGGTGTTTAAAAGGTTTTA 12 16 1 AGGGTGTTTA 0.958253 -35 CCTTCGGGACAGGGTCTTAAGCCCTGCGCC 17 229 1 AGGGTCTTAA 0.636301 -72 ACAGTGTTTTTTTGATTTTA 18 181 0 ACAGTGTTTT 0.933519 -10 ********** Masking position 5 Map Score: 9.48168 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 67 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TTTTGAAAATGCAATCAAAAATGCATAATG 2 66 0 GCAATCAAAA 0.977069 -74 AACTTAGTCAGCAATCAACATCTACCTTTT 3 38 0 GCAATCAACA 0.960204 -25 TGGCAATATTGCAATATAAATTTTCCGACG 7 125 0 GCAATATAAA 0.787104 -30 CCCCTTGAATGCAAAAAAATATATATCGAA 10 11 0 GCAAAAAAAT 0.697393 -167 TCAACGGAACGCAATCAACAACAAAA 14 7 0 GCAATCAACA 0.960204 -139 GACTCTTACTGCAGTAAAAAGCATGCGGGG 17 176 1 GCAGTAAAAA 0.921151 -125 AAGGATTAGTGCAGTCAAATTTAATAATTT 18 21 1 GCAGTCAAAT 0.937658 -170 TAAGTGATTAGCAATTAAATATAACTCAGT 18 64 1 GCAATTAAAT 0.835787 -127 ********** Masking position 3 Map Score: 3.73667 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 80 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 ACACCGTAAAAAAAACGAAAAA 4 3 0 AAAAACGAAA 0.558372 -97 AAACATTGTTAGCCAGAAAGGTTCTGGCAA 4 67 1 AGCCAGAAAG 0.882018 -33 CTACAAACTTAAAAAGCAAATTAGTTTTAA 7 79 0 AAAAAGCAAA 0.692834 -76 GGTAAGCTTAAACCAGAAAGCGCAAATTTC 9 68 0 AACCAGAAAG 0.90063 -71 GAACATTCTCAGCAAGAAAACATTTAAAAC 11 43 1 AGCAAGAAAA 0.922357 -39 GAACGCAATCAACAACAAAA 14 1 0 AACAACAAAA 0.814359 -145 TAATCTATCGAAACAGAAAAAGAAATATTC 14 58 1 AAACAGAAAA 0.904192 -88 GGGGTTGCCGAGCCAGGAAAAGGCGCAGGG 17 250 0 AGCCAGGAAA 0.896487 -51 CTTAAAAGACAAAAAGAAAATTATTAAATT 18 38 0 AAAAAGAAAA 0.879958 -153 ********** Masking position 5 Map Score: 1.15735 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 208 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 CTAAAATATTAGGAAAAATTG 5 2 0 AGGAAAAATT 0.962729 -57 TTTTATCTTAAAGAAAAATTTAAATATCGT 7 47 0 AAGAAAAATT 0.942617 -108 TTCCGACGTACAGAAAAATTCAAGCTACAA 7 103 0 CAGAAAAATT 0.946619 -52 TTCTGTACGTCGGAAAATTTATATTGCAAT 7 118 1 CGGAAAATTT 0.873082 -37 GAAACAGAAAAAGAAATATTCACAAAAGGT 14 67 1 AAGAAATATT 0.80207 -79 AACCCCCGCTTGGAAAAATTTGAGAATTGC 17 274 1 TGGAAAAATT 0.910897 -27 ********** Masking position 5 Map Score: 1.17061 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 68 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 CCCATCACCACCCCAAACACTGTT 2 5 1 TCACCACCCC 0.93378 -135 TTTCCACCTCCTCTTGCCAG 4 90 0 TTTCCACCTC 0.965414 -10 GGCTTCCCCTTCTCAACCTCACGCCTCTCA 6 43 1 TCTCAACCTC 0.931639 -258 ACCTTATCCTTCTTCACCTCGAAACTTCCC 6 121 1 TCTTCACCTC 0.965414 -180 TGAAAAATCTTCACCAATTCTCAAATACAT 10 78 1 TCACCAATTC 0.825985 -100 GGGCTTCAACTCTAAGTGTATT 10 166 0 GCTTCAACTC 0.743462 -12 GCTTCGCTCTCTCCAATTCGTTTTAAATG 11 63 0 TCTCCAATTC 0.916045 -19 CCGCTTTAATTTCCCACCTCAATCCAGGTG 17 23 1 TTCCCACCTC 0.910766 -278 ********** Masking position 6 Map Score: 2.29966 Number of sites scoring better than the average of aligned sites = 1283 Number in coding regions = 1203 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 12 CTAATATTTTAGGGAAAAACCTTATGACCTTG 5 20 1 AGGAAAACCT 0.953339 -39 TTTTTCTTTAAGATAAAAACTTAAAACTAATT 7 59 1 AGTAAAACTT 0.965002 -96 GAAAAATTCAAGCTACAAACTTAAAAAGCAAA 7 89 0 AGTAAAACTT 0.965015 -66 GTTGTGGGAAGGTTAAAAAACTTCTCGATTGC 9 109 0 GGTAAAAACT 0.832485 -30 CCCATTTAATGGGAAAAAACTTAAATAAAATG 11 12 0 GGAAAAACTT 0.820778 -70 AAAATCTTTCAGTTATAAACCTTTTGTGAATA 14 83 0 AGTAAAACCT 0.970031 -63 TCTCAATTTTAGGTAATAACCTATAAACTTTT 18 96 1 AGTATAACCT 0.903268 -95 ** ** ****** Masking position 5 Map Score: 1.03442 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 43 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 GGAATCCTGCCACTCTCAGCC 6 2 1 GAATCCTGCC 0.980416 -299 TTGAGAAGGGGAAGCCTGAGCTTATAAGGC 6 29 0 GAAGCCTGAG 0.980416 -272 AAATCCTCATGTATCCTGACGGTAAGGTTT 10 135 1 GTATCCTGAC 0.937095 -43 CACCCTTGCCGAAGCTTGAGC 12 2 0 GAAGCTTGAG 0.885643 -49 CCGCGGGTTCGAATCCCGCCCCCCGCATGC 17 196 0 GAATCCCGCC 0.948199 -105 CTAAAATTGAGAATACTGAGTTATATTTAA 18 78 0 GAATACTGAG 0.903303 -113 ********** Masking position 3 Map Score: 0.74617 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 163 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 CAGCCTGTAAATTCAATGGGCGATTTAAGC 1 31 0 ATTCAATGGG 0.973462 -93 ATTTTTTTGCATTCAAGGGGATTTGTTAAA 10 21 1 ATTCAAGGGG 0.982681 -157 GTTTTTTCCCATTAAATGGGAACATTCTCA 11 24 1 ATTAAATGGG 0.959538 -58 GAGGTGGGAAATTAAAGCGGTGATTCGCCT 17 13 0 ATTAAAGCGG 0.931898 -288 ********** Masking position 5 Map Score: 0.309545 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 10 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 ********** 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