AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iargR_mthe_opreg_100.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 MTH179 117 unknown #2 MTH181 49 unknown #3 MTH182 36 glutamate N-acetyltransferase #4 MTH255 269 ribosomal protein L7a #5 MTH256 49 ribosomal protein S28 #6 MTH261 24 translation initiation factor eIF-2, gamma subunit #7 MTH262 24 conserved protein #8 MTH846 170 N-acetyl-gamma-glutamyl-phosphate reductase #9 MTH997 31 carbamoyl-phosphate synthase, large subunit #10 MTH1254 135 argininosuccinate synthase #11 MTH1337 81 N-acetylornithine aminotransferase #12 MTH1445 64 glycinamide ribonucleotide synthetase Motif number 1 TGTAATATGTATTATATGAGTTAATATCTTT 1 46 0 ATTATAGAGT 0.707757 -72 CTTCAAGATAATATTAAGGGGAATTGAA 2 32 1 ATATTAGGGG 0.7951 -18 CAGCGAACTTTTTTTACGGGAGA 3 24 1 TTTTTAGGGA 0.930144 -13 TTGCTGCCAATTAAAAAGGGAAGGAATAATG 4 25 0 TTAAAAGGGA 0.684337 -245 GCAGCAAAACTTTATATGTGATGAAGCTTTA 4 49 1 TTTATAGTGA 0.900576 -221 CAATTTCAATTTAATAAAGGTGATTTA 5 33 1 TTAATAAGGT 0.897564 -17 TAAAAGCGTTTATAGGTGTAATCT 6 9 1 TTTATAGTGT 0.912994 -16 AGTGATGGACATTATATGGGTGGGAGGCCCC 8 85 1 ATTATAGGGT 0.96849 -86 AGTGATGGACATTATATAGGTGGGTATAG 8 152 1 ATTATAAGGT 0.90755 -19 GGGAATATTAGATGAGAGGAATGGG 9 5 1 ATATTAATGA 0.361988 -27 TATGGGATAAGTTATAAGTGTATGTCCCACC 10 56 0 GTTATAGTGT 0.71029 -80 ACTATAGATATTAATATGGGATAAGTTATAA 10 70 0 TTAATAGGGA 0.959484 -66 AGGTTCAACATTAATACAGGTCCCCATATAA 11 46 1 TTAATAAGGT 0.897564 -36 TCACCAAAAATTTATATGGGGACCTGTATTA 11 57 0 TTTATAGGGG 0.951891 -25 GAAAGTATATATTTTATAGGAAATATGTCAT 12 38 0 ATTTTAAGGA 0.763547 -27 ****** **** Masking position 6 Map Score: 15.2862 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 400 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 CCTCAAACTGAGGGGTAAAGATATTAACTCAT 1 30 1 AGGGGTAGAT 0.963787 -88 TACATATTACATTGATGAGGATTCCATGAGAA 1 66 1 ATTGATGGAT 0.960504 -52 GGAAGGAATAATGGATGCAGATGAGAG 4 6 0 ATGGATAGAT 0.987632 -264 ATAAAACTTGCTGGATACAGATTTTCATGAGA 4 146 0 CTGGATAGAT 0.943448 -124 AATCCAAGTTATGGATTAACATGAAGTGGGTG 4 202 0 ATGGATACAT 0.972466 -68 AACTTGGATTATTGATCCAGATTGGTGTAATT 4 224 1 ATTGATAGAT 0.971553 -46 CGACCGGGTCAGTGATGGACATTATATGGGTG 8 75 1 AGTGATACAT 0.960264 -96 TACCCAGGTCAGTGATGGACATTATATAGGTG 8 142 1 AGTGATACAT 0.960264 -29 ATTAGATGAGAGGAATGGGGATAAA 9 17 1 AGGAATGGAT 0.899081 -15 CACCTGCCGCAGGTATACGGATTTTTCCGGAA 10 28 0 AGGTATGGAT 0.898938 -108 ****** **** Masking position 6 Map Score: 11.277 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 260 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 CTGCCGGGACGGTCTCATCCCTCA 1 5 1 CGGGACGGTC 0.822362 -113 AATCAGGTGCAGGGAGAGAGCA 1 106 1 AGGGAGAGAG 0.735896 -12 ATAATGGATGCAGATGAGAG 4 1 0 CAGATGAGAG 0.94111 -269 TAACATGAAGTGGGTGAGTACCTTTATATG 4 188 0 TGGGTGAGTA 0.896326 -82 ATTATTGATCCAGATTGGTGTAATTACCGA 4 231 1 CAGATTGGTG 0.739979 -39 TGGCCACGACCGGGTCAGTGATGGACATTA 8 69 1 CGGGTCAGTG 0.978562 -102 GGACATTATATGGGTGGGAGGCCCCACCAT 8 91 1 TGGGTGGGAG 0.98023 -80 CCAGAGTACCCAGGTCAGTGATGGACATTA 8 136 1 CAGGTCAGTG 0.97144 -35 GGACATTATATAGGTGGGTATAG 8 158 1 TAGGTGGGTA 0.896326 -13 GGGAATATTAGATGAGAGGAATGGGGAT 9 9 1 TAGATGAGAG 0.87212 -23 ATACCTGCGGCAGGTGGGACATACACTTAT 10 44 1 CAGGTGGGAC 0.963465 -92 ********** Masking position 3 Map Score: 8.21026 Number of sites scoring better than the average of aligned sites = 956 Number in coding regions = 894 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 TCCCGTAAAAAAAGTTCGCTGGGGTCGTCTC 3 14 0 AAATTCGCTG 0.967431 -23 ATCACATATAAAGTTTTGCTGCCAATTAAAA 4 40 0 AAGTTTGCTG 0.9734 -230 CTCGGTATATAAAACTTGCTGGATACAGATT 4 155 0 AAACTTGCTG 0.973401 -115 AAAAAATTGGTGTCTATGACCA 7 13 0 AAAATTGGTG 0.961076 -12 AAATACTTATAAATTTTGGTGGCCACGACCG 8 50 1 AAATTTGGTG 0.98784 -121 TCCCCATATAAATTTTTGGTGATATC 11 66 1 AATTTTGGTG 0.961076 -16 *** ******* Masking position 6 Map Score: 4.70628 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 4 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 CTGCCGGGACGGTCTCATCCCTCAAACTGAGGGG 1 11 1 GGTCTCCTCA 0.907052 -107 TGGGAGACGACCCCAGCGAACTTTT 3 2 1 GGGAGCCCCA 0.993709 -35 GGTGGTCATAGACACCAATTTTTT 7 4 1 GGTCACACCA 0.975677 -21 GGGGAAGATATCCCCATGGACAGTTA 8 3 1 GGAAGCCCCA 0.987784 -168 TCACTGACCCGGTCGTGGCCACCAAAATTTATAA 8 56 0 GGTCGCACCA 0.995177 -115 TTATATGGGTGGGAGGCCCCACCATACCCTCGCA 8 96 1 GGGAGCACCA 0.99121 -75 ***** ***** Masking position 14 Map Score: 3.46004 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 100 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ACTGAGGGGTAAAGATATTAACTCATATAAT 1 36 1 AAAGATATTA 0.948675 -82 AAAGAAATCTATTTAAGGATA 2 1 1 AAAGAAATCA 0.871113 -49 ACAAGGATTAATAGAAATTAAAGCTTCATCA 4 67 0 ATAGAAATTA 0.97182 -203 CCTTTATTAAATTGAAATTGAAAGGCTTTTA 5 22 0 ATTGAAATTA 0.894829 -28 TTACAGCACTATAGATATTAATATGGGATAA 10 77 0 ATAGATATTA 0.97182 -59 TAAACTGATAATAAATATTTATGTTGAGGTG 11 16 0 ATAAATATTA 0.842142 -66 ********* * Masking position 5 Map Score: 1.6025 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 26 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 AAGTTCGCTGGGGTCGTCTCCCA 3 2 0 GGGCTCTCCC 0.994401 -35 CTTGTTTTCCTGGGCGTCTTACTGGATGATCC 4 93 1 TGGCTCTTAC 0.967987 -177 CTGGTTTTTCTACCATCCATCGGT 4 256 0 GGTTTCTACC 0.870667 -14 ACTGTCCATGGGGATATCTTCCCC 8 3 0 GGGTTCTTCC 0.975637 -168 AGGGTATGGTGGGGCCTCCCACCCATATAATG 8 94 0 GGGCTCCCAC 0.984883 -77 CTGAATTGCTGGCCCACTTCCGGAAAAATCC 10 10 1 TGGCACTTCC 0.928394 -126 AAGTTATAAGTGTATGTCCCACCTGCCGCAGG 10 47 0 TGTTTCCCAC 0.808644 -89 *** * ****** Masking position 8 Map Score: 1.85816 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 570 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 AGAACTATTCTCATGGAATCCTCATCAATGT 1 74 0 TCATGGAATC 0.916395 -44 ATACGATTTCTCATGAAAATCTGTATCCAGC 4 138 1 TCATGAAAAC 0.885904 -132 CTCACCCACTTCATGTTAATCCATAACTTGG 4 200 1 TCATGTTAAC 0.581845 -70 GGTGGTCATAGACACCAATTTTTT 7 6 1 TCATAGACAC 0.954125 -19 GAAGATATCCCCATGGACAGTTAAAGGTTGT 8 14 1 CCATGGACAT 0.942014 -157 TATAAGTATTTCATGGACAACCTTTAACTGT 8 30 0 TCATGGACAC 0.995309 -141 ACTGACCCGGTCGTGGCCACCAAAATTTATA 8 57 0 TCGTGGCCAC 0.929407 -114 ACCGGGTCAGTGATGGACATTATATGGGTGG 8 77 1 TGATGGACAT 0.954912 -94 CCCAGGTCAGTGATGGACATTATATAGGTGG 8 144 1 TGATGGACAT 0.954912 -27 ********* * Masking position 4 Map Score: 5.69586 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 621 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 GGATTCCATGAGAATAGTTCTCAATCAGGTG 1 84 1 AGAATATTCT 0.846469 -34 AATCTATTTAAGGATACTTCAAGATAATATT 2 16 1 AGGATATTCA 0.944096 -34 TGGATGATCCGGGATAATTCAGAATACGATT 4 115 1 GGGATATTCA 0.98386 -155 ATATTAATATGGGATAAGTTATAAGTGTATG 10 63 0 GGGATAGTTA 0.906643 -73 CTTATAAATGGAATCATTCTGATACGCTCA 10 116 0 GGAATCTTCT 0.896877 -20 CTTGAACGGAATCTGTCATTATTATTAA 12 8 1 GGAATCGTCA 0.976581 -57 TATTTTATAGGAAATATGTCATTAATAATAA 12 29 0 GAAATAGTCA 0.889407 -36 ****** **** Masking position 4 Map Score: 1.75224 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 191 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 ********** No masking Map Score: -2.17893e-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 11 ********** No masking Map Score: -2.17893e-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: -2.17893e-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