AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iargR_pyro_opreg_300.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0726 129 317aa long hypothetical ornithine carbamoyltransferase #2 PH1153 300 354aa long hypothetical protein #3 PH1255 105 180aa long hypothetical protein #4 PHS034 44 65aa long hypothetical zinc finger protein #5 PH1257 47 227aa long hypothetical protein #6 PH1501 96 438aa long hypothetical aminotransferase #7 PH1721 215 273aa long hypothetical ribosomal protein S6 modification protein Motif number 1 GCCGGACTTTCTCCACTTCCAGGATTAGGA 2 191 0 CTCCACTTCC 0.981009 -110 ATCGGAGAGTGCCCACCTTCGTCATCGGCC 2 218 0 GCCCACCTTC 0.885068 -83 TGGCTCCTCGCCCCACATCCTCATCAAATC 2 245 0 CCCCACATCC 0.988661 -56 GTCCCCACCATCGGTAAAAGTT 3 94 0 CCCCACCATC 0.980547 -12 TTTACCTCCCCATCCTTGAGTTGTC 4 30 0 CTCCCCATCC 0.98079 -15 ATACAGGACACTCCGCTTTCATCTCTATCC 7 19 0 CTCCGCTTTC 0.917628 -197 TCTATCTCAGCTCCACATACAGGACACTCC 7 35 0 CTCCACATAC 0.982904 -181 TCTGGTGTAGCTCAACGTTCTCAAGCTCTA 7 61 0 CTCAACGTTC 0.931471 -155 ATACAGGACACTCAACGATCTGGTGTAGCT 7 79 0 CTCAACGATC 0.896751 -137 TCAAGCTCAGCTCCACATACAGGACACTCA 7 95 0 CTCCACATAC 0.982904 -121 CCTCTGGAACCTCCTCCAACACCAATGGGT 7 139 0 CTCCTCCAAC 0.909171 -77 CCCCCCAATCCTCCTCGACCTCTGGAACCT 7 157 0 CTCCTCGACC 0.953861 -59 AAGGGCTACTCCCCCCAATCCTCCTCGACC 7 167 0 CCCCCCAATC 0.956733 -49 ********** Masking position 6 Map Score: 21.6299 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 575 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 2 AATACTCAATCCCCTCCGAAACTTTT 1 5 1 CTATCCCCTC 0.929 -125 CCCTCCGAAACTTTTTAACTTATTAAAACTTC 1 22 1 CTTTAACTTA 0.853345 -108 TAACAACCATCTTTCTCACCTCCATTATTATC 2 29 1 CTTTCACCTC 0.994771 -272 GTTATAAAGCCTCTGGCTCCTCGCCCCACATC 2 256 0 CTTGCTCCTC 0.943389 -45 GAGCCAGAGGCTTTATAACTTCATTCCTCCAT 2 269 1 CTTTAACTTC 0.953752 -32 AGATCCATACCTTTAAAACCTAGGTATTAACT 3 66 1 CTTAAACCTA 0.857793 -40 CGGTCAAAAGCTATATAAGCTATTTTGACATT 6 40 1 CTTTAAGCTA 0.900006 -57 CCGCTTTCATCTCTATCCCCCCGTAA 7 5 0 CTTTCCCCCC 0.950963 -211 TTCTCAAGCTCTATCTCAGCTCCACATACAGG 7 42 0 CTTTCAGCTC 0.980721 -174 CCTCCTCGACCTCTGGAACCTCCTCCAACACC 7 146 0 CTTGAACCTC 0.98314 -70 ** * ******* Masking position 2 Map Score: 9.32663 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 479 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 CTCCGAAACTTTTTAACTTATTAAAACTTC 1 24 1 TTTTAACTTA 0.811939 -106 TTTTAACTTATTAAAACTTCATACCTGAGC 1 34 1 TTAAAACTTC 0.960991 -96 GAAACGATTATTAAAACTCAAGCCTAAGTG 1 94 1 TTAAAACTCA 0.927934 -36 TTAAAGTACATTTAAAATTATTTGGCATAA 2 145 0 TTTAAAATTA 0.798536 -156 GCCAGAGGCTTTATAACTTCATTCCTCCAT 2 271 1 TTATAACTTC 0.943905 -30 AACGAGAAGTTTATAAATCC 3 1 0 TTATAAATCC 0.856632 -105 ATCCATACCTTTAAAACCTAGGTATTAACT 3 68 1 TTAAAACCTA 0.825848 -38 AAACTTTTATAAATACCCTGACAACT 4 7 1 TTATAAATAC 0.794283 -38 TGTTTCATCATTAAAAATAAAAA 5 4 0 TTAAAAATAA 0.83907 -44 CCTCCAAAAATTAAAAATTAAAAAGGGCTA 7 189 0 TTAAAAATTA 0.934459 -27 ********** Masking position 5 Map Score: 8.17003 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 164 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 TAAAAAGTTTCGGAGGGGATTGAGTATT 1 9 0 CGGAGGGGAT 0.947604 -121 TAGATAATAATGGAGGTGAGAAAGATGGTT 2 33 0 TGGAGGTGAG 0.992844 -268 CGGCCGATGACGAAGGTGGGCACTCTCCGA 2 217 1 CGAAGGTGGG 0.819676 -84 GATGAGGATGTGGGGCGAGGAGCCAGAGGC 2 250 1 TGGGGCGAGG 0.924537 -51 TAATGTTTCATGGAGGAATGAAGTTATAAA 2 280 0 TGGAGGAATG 0.792703 -21 CTTTTACCGATGGTGGGGAC 3 96 1 TGGTGGGGAC 0.861948 -10 GTCCTGTATGTGGAGCTGAGATAGAGCTTG 7 40 1 TGGAGCTGAG 0.98183 -176 GTCCTGTATGTGGAGCTGAGCTTGAAGTGG 7 100 1 TGGAGCTGAG 0.98183 -116 CCATTGGTGTTGGAGGAGGTTCCAGAGGTC 7 141 1 TGGAGGAGGT 0.933007 -75 TCGAGGAGGATTGGGGGGAGTAGCCCTTTT 7 169 1 TTGGGGGGAG 0.902297 -47 TTTTAATTTTTGGAGGGAGGTGA 7 203 1 TGGAGGGAGG 0.986514 -13 ********** Masking position 5 Map Score: 12.2625 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 644 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 TCAAATCGGAGAGTGCCCACCTTCGTCATC 2 222 0 GAGTGCCCAC 0.924063 -79 GATGTGGGGCGAGGAGCCAGAGGCTTTATA 2 256 1 GAGGAGCCAG 0.96115 -45 CCCCATCCTTGAGTTGTCAGGGTATTTATA 4 18 0 GAGTTGTCAG 0.871466 -27 ATCATCCCATCAGGGTCCTGGCTGTTTCAT 5 26 0 CAGGGTCCTG 0.562615 -22 GATGAAAGCGGAGTGTCCTGTATGTGGAGC 7 26 1 GAGTGTCCTG 0.976795 -190 CCAGATCGTTGAGTGTCCTGTATGTGGAGC 7 86 1 GAGTGTCCTG 0.976795 -130 GGTGTTGGAGGAGGTTCCAGAGGTCGAGGA 7 146 1 GAGGTTCCAG 0.983374 -70 ********** Masking position 2 Map Score: 6.80489 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 129 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 TGGGTTCCTAATCCTGGAAGTGGAGAAAGT 2 186 1 ATCCTGGAAG 0.932996 -115 ATGATGAAACAGCCAGGACCCTGATGGGAT 5 23 1 AGCCAGGACC 0.952944 -25 TAGCAAAATTATACTGGAAAGATTATTGAA 6 72 1 ATACTGGAAA 0.956502 -25 TCAGCTCCACATACAGGACACTCCGCTTTC 7 29 0 ATACAGGACA 0.986109 -187 TCAGCTCCACATACAGGACACTCAACGATC 7 89 0 ATACAGGACA 0.986109 -127 ********** Masking position 8 Map Score: 1.59663 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 28 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TTATTATCTACTACTATAGTGTATAAAAGGTTTT 2 53 1 CACTATGTAT 0.972163 -248 TTAATTATTTCGACGATTGTCAATCCTAATTTTA 2 101 0 CACGATGTAT 0.994546 -200 TTGGCATAAACAATGATGGTTAATTATTTCGACG 2 120 0 CATGATGTAT 0.987794 -181 AACGTTGTATCAATGTTCGTTAATCAACGATATT 3 32 1 CATGTTGTAT 0.960934 -74 GTTCGTTAATCAACGATATTAGATCCATACCTTT 3 46 1 CACGATTTAT 0.972177 -60 * ***** ** ** Masking position 7 Map Score: 1.09471 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 6 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 ********** No masking Map Score: -6.79689e-13 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 9 ********** No masking Map Score: -6.79689e-13 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 10 ********** No masking Map Score: -6.79689e-13 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