AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_aful_reg_300.orf -o00340_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 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 = 1 Purged sequences: AF0212 25 histidinol dehydrogenase (hisD) Input sequences: #1 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #2 AF0590 185 ATP phosphoribosyltransferase (hisG) #3 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #4 AF0818 102 acylphosphatase (acyP) #5 AF0986 30 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA-2) #6 AF0987 109 conserved hypothetical protein #7 AF1642 50 histidyl-tRNA synthetase (hisS) #8 AF1778 105 stage V sporulation protein (spoVG) #9 AF1779 57 2-hydroxyacid dehydrogenase, putative #10 AF1942 201 A. fulgidus predicted coding region AF1942 #11 AF1946 136 cysteine proteinase, putative #12 AF1948 152 A. fulgidus predicted coding region AF1948 #13 AF1950 54 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (hisIE) #14 AF2265 48 imidazoleglycerol-phosphate synthase, subunit H (hisH) Motif number 1 TTATACCTTTCGTTTACCATCCTGGCATCTTT 1 77 0 CTTTACCACC 0.944268 -47 GCTTATAAAACCCACCGCTTTAA 2 2 1 CTATAAAACC 0.845752 -184 CTGACGGTCATCTTGAAAAGCCAATCTGGGAC 2 77 1 TTTGAAAACC 0.963906 -109 CCCCTCTCCGTCTTTCCAAGCCTGTATCCAGC 2 121 0 TTTTCCAACC 0.928938 -65 ACCTCATTGACGTTGACCACCCCAAGCTGGTT 2 155 1 CTTGACCACC 0.89004 -31 CTGCTTAAAAACCAGCTTGGGGT 2 173 0 TCTTAAAACC 0.9663 -13 AAATAAATCTTACTGAAAATCCAAAAAATTTA 3 54 0 TCTGAAAACC 0.932049 -44 TCAATAACTATTTTGAAAAACTTTTTATTGAT 6 31 0 TTTGAAAACT 0.713394 -79 ACTCTAAAACCTTTTAAACACCCTTGCCGAAG 7 22 1 CTTTAAACCC 0.89043 -29 GTTTGGCTTTTGCTTCAAAACCTTTTTATCTT 9 17 1 TCTTCAAACC 0.906813 -41 TTGCTCATGCTCTTTAAAAATCAAGCGATTCG 10 20 1 TTTTAAAATC 0.734906 -182 ATAAAATTTGCCTTTAAAACCCTCATTAACAC 11 53 0 CTTTAAAACC 0.986386 -84 AGTAATTCATCCCTTAAAAACTGTTGGAACGG 11 87 1 CCTTAAAACT 0.776211 -50 CTTTTCATTTTTTAAAATCAGTGGACTTTT 12 9 1 TTTTAAAACA 0.747135 -144 CTCCAATTTTCCATTAAAAGCCCACAAAACTT 12 94 1 CATTAAAACC 0.877012 -59 GCCCACAAAACTTTTCGAAACCTATTTAAAGA 12 113 1 CTTTCGAACC 0.79524 -40 ATTCTATTTTTTACAACACAAAAACCTAT 13 8 1 TTTTACAAAC 0.656003 -47 CAAAAACCTATTTTTACCACCCGGCCAATTTA 13 29 1 TTTTACCACC 0.928939 -26 * ******* ** Masking position 4 Map Score: 16.5306 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 431 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 AAGTAGACCTTGACCTTTTCGTTCTGCATC 2 46 0 TGACCTTTTC 0.784469 -140 TGACTTTATTTAAATTTTTTGGATTTTCAG 3 44 1 TAAATTTTTT 0.715045 -54 TTTTTTAACCTTTTCTTCCCACTCC 5 6 1 TAACCTTTTC 0.961465 -25 ACTATTTTGAAAAACTTTTTATTGATAAAT 6 27 0 AAAACTTTTT 0.949962 -83 ACCTCCGGACAAAGCTATTTATAAGTGATT 6 77 1 AAAGCTATTT 0.713516 -33 CTCAACTCTAAAACCTTTTAAACACCCTTG 7 18 1 AAACCTTTTA 0.902185 -33 TTTTGCTTCAAAACCTTTTTATCTTTTCTG 9 24 1 AAACCTTTTT 0.982961 -34 TTATTTTAGTAAAATTTTTTTACTTATAAA 10 102 0 AAAATTTTTT 0.849926 -100 AAAAGCCCACAAAACTTTTCGAAACCTATT 12 109 1 AAAACTTTTC 0.959272 -44 AAACTTTTCGAAACCTATTTAAAGAAAAAG 12 120 1 AAACCTATTT 0.944865 -33 GAAAAATTTTTAACTTTTTCTTTAAATAGG 12 133 0 TAACTTTTTC 0.866098 -20 GAAAAAGTTAAAAATTTTTC 12 143 1 AAAATTTTTC 0.859867 -10 TACAACACAAAAACCTATTTTTACCACCCG 13 22 1 AAACCTATTT 0.944865 -33 AACCTTAATTAATCCTTTTTCTCAAGCCCT 14 25 1 AATCCTTTTT 0.852173 -24 ********** Masking position 6 Map Score: 16.5848 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 388 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 CTTTTTACCCAAAAAACATGCAGCCTGTAAA 1 50 0 AAAAAACATC 0.777627 -74 GCTTATAAAACCCACCGCTTTAACAC 2 6 1 TAAAACCCAC 0.954194 -180 GCTTTAACACTAAAGCCATGATGCAGAACGA 2 27 1 TAAAGCCATA 0.795783 -159 GGTCATCTTGAAAAGCCAATCTGGGACGCCT 2 82 1 AAAAGCCAAC 0.979071 -104 CTGCTTAAAAACCAGCTTGGGGTGGT 2 170 0 TAAAAACCAC 0.854603 -16 AAAATTTAAATAAAGTCAATCTGACACAAGC 3 31 0 TAAAGTCAAC 0.869984 -67 AATCTTACTGAAAATCCAAAAAATTTAAATA 3 50 0 AAAATCCAAA 0.700082 -48 GTTTTGAAGCAAAAGCCAAACTCTTAA 9 7 0 AAAAGCCAAC 0.979071 -51 GAGCATGAGCAAAAAACAACC 10 1 0 AAAAAACAAC 0.907714 -201 CATGCTCTTTAAAAATCAAGCGATTCGGTGT 10 25 1 AAAAATCAAC 0.872843 -177 AATTTGCCTTTAAAACCCTCATTAACACAGT 11 50 0 TAAAACCCTA 0.704911 -87 ATTTTCCATTAAAAGCCCACAAAACTTTTCG 12 99 1 AAAAGCCCAA 0.925445 -54 ********* * Masking position 4 Map Score: 9.761 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 322 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 CCTGTATCCAGCGGTAATTAAGGCGTCCCAG 2 102 0 GCGGTATTAA 0.988567 -84 CCTTTTGCCTGCGGTATATAAGTTTGAATTC 4 75 0 GCGGTAATAA 0.983699 -28 TTATGAGAGCGTGGTAATTTAATCTAACGTT 8 18 1 GTGGTATTTA 0.944416 -88 CTCAAACAAAGTGGTATATAAGAATTTTGAT 8 56 0 GTGGTAATAA 0.975008 -50 GTGGTTGAATGAGGTAGTTAATTCCGTTAAC 10 165 1 GAGGTATTAA 0.96942 -37 ****** **** Masking position 6 Map Score: 3.07864 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 GGTGGTCAACGTCAATGAGGTATCCCCTCT 2 146 0 GTCAATGAGG 0.979935 -40 AAGCGATTCGGTGTATGATGATAGTGTATG 10 42 1 GTGTATGATG 0.975933 -160 TATGATGATAGTGTATGATGGTACTCACAA 10 55 1 GTGTATGATG 0.975933 -147 CTAAGGGTGGTTGAATGAGGTAGTTAATTC 10 159 1 TTGAATGAGG 0.961666 -43 ATGTGACTGTGTTAATGAGGGTTTTAAAGG 11 45 1 GTTAATGAGG 0.970545 -92 ********** Masking position 5 Map Score: 3.03506 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 65 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TTAGTGTTAAAGCGGTGGGTTTTATAAGC 2 9 0 AGGGTGGGTT 0.972214 -177 ACCGCAGGCAAAAGGTGGGGTT 4 91 1 AAGGTGGGGT 0.953767 -12 GGAGGTAGGGATTGATGGTTTCAATAACTAT 6 52 0 ATGATGGTTT 0.932973 -58 ACGAAATTTGAAAGGAGGGTTAGAA 8 91 1 AAGGAGGGTT 0.971226 -15 GTTCTCAACTAAGGGTGGTTGAATGAGGTAG 10 151 1 AAGGTGGTTG 0.954643 -51 TGACTGTGTTAATGAGGGTTTTAAAGGCAAA 11 48 1 AAGAGGGTTT 0.868891 -89 TGTTCTGACCATCGGTGGTTTG 11 125 1 ATGGTGGTTT 0.983833 -12 TTAATGGAAAATTGGAGGTTTAGGGAAGTCT 12 80 0 ATGGAGGTTT 0.963602 -73 ** ******** Masking position 1 Map Score: 6.44709 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 146 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 GATTTTCAGTAAGATTTATTTAACTGAGTT 3 65 1 AAGATTTATT 0.882793 -33 TGCGGTATATAAGTTTGAATTCTTTTGTAT 4 67 0 AAGTTTGAAT 0.912248 -36 AGATTAATGAAGATTGATTTATCAATAAA 6 10 1 AAGATTGATT 0.957403 -100 GGTATATAAGAATTTTGATTGCAGGAAACG 8 45 0 AATTTTGATT 0.933853 -61 AGCTATCCTCAATTTTTATTTTAGTAAAAT 10 117 0 AATTTTTATT 0.824483 -85 GGGAAGTCTAAAGTATGATTTTCGAACTTC 12 59 0 AAGTATGATT 0.911737 -94 ********** Masking position 6 Map Score: 1.65134 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 56 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 ATGCAGCCTGTAAATTCAATGGGCGATTTAA 1 33 0 TAAATCAATG 0.985149 -91 AAAATTTAAATAAAGTCAATCTGACACAAGC 3 31 0 TAAATCAATC 0.961158 -67 GCTGCAACTCTAAACTCAGTTAAATAAATCT 3 76 0 TAAATCAGTT 0.947433 -22 ATCAATGTATTAAAGTCAATGTGACTGTGTT 11 27 1 TAAATCAATG 0.985148 -110 TTTCATTTTTTAAAATCAGTGGACTTTTAAC 12 13 1 TAAATCAGTG 0.986227 -140 **** ****** Masking position 6 Map Score: 3.62044 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 CAAAGGAGCGAAAATTTAAAA 1 1 0 AAAATTAAAA 0.940675 -123 CTGAAAATCCAAAAAATTTAAATAAAGTCAA 3 43 0 AAAAATTTAA 0.613202 -55 GAACGAATTGAAATCATATAAATAGTTTGCC 4 26 0 AAATATATAA 0.772522 -77 AGTGGGAAGAAAAGGTTAAAAAA 5 3 0 AAAGTTAAAA 0.767808 -28 AAAACTGATAATAAATCACTT 6 99 0 AAAATGATAA 0.878517 -11 TTGAACCCAGAAAAGATAAAAAGGTTTTGAA 9 30 0 AAAAATAAAA 0.920115 -28 TCTGAAGGATAAAATTTATAAGTAAAAAAAT 10 88 1 AAAATTATAA 0.949603 -114 TACATTGATAAAAATAAATAAAAGA 11 5 0 AAAAAAATAA 0.658224 -132 TTTTAAAGGCAAATTTTATAAAGTAATTCAT 11 66 1 AAATTTATAA 0.823793 -71 ACTGATTTTAAAAAATGAAAAG 12 2 0 AAAATGAAAA 0.858868 -151 TATTTAAAGAAAAAGTTAAAAATTTTTC 12 135 1 AAAATTAAAA 0.940675 -18 TTTGTGTTGTAAAAAATAGAAT 13 2 0 AAAAATAGAA 0.808117 -53 **** ****** Masking position 3 Map Score: 9.57509 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 60 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 10 TAAATGAATCCTTAAGCCCTTTTCTTCT 1 106 1 CTTAAGCCCT 0.958385 -18 GTCAATCTGACACAAGCTCAAGAAATCTGG 3 18 0 CACAAGCTCA 0.930518 -80 GCTCAAGCTTCGGCAAGGGTG 7 40 0 CTCAAGCTTC 0.926002 -11 TTGTTTTTTGCTCATGCTCTTTAAAAATCA 10 13 1 CTCATGCTCT 0.971296 -189 AATCCTTTTTCTCAAGCCCTTGCG 14 35 1 CTCAAGCCCT 0.991748 -14 ********** Masking position 4 Map Score: 0.457771 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 349 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 CCCACCGCTTTAACACTAAAGCCATGATGC 2 21 1 TAACACTAAA 0.913062 -165 TGCTGCAACTCTAAACTCAGTTAAA 3 83 0 CAACTCTAAA 0.98355 -15 AAATTCGCTCAACTCTAAAACCTTTTAAA 7 10 1 CAACTCTAAA 0.98355 -41 AGCAAAAGCCAAACTCTTAA 9 1 0 AAACTCTTAA 0.820598 -57 CTATTTTTTACAACACAAAAACCTATTTTT 13 14 1 CAACACAAAA 0.926915 -41 ********** Masking position 3 Map Score: 1.85001 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 19 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 12 ********** No masking Map Score: -2.75447e-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: -2.75447e-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: -2.75447e-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