AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iarcA_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 PH0016 300 475aa long hypothetical protein #2 PH0623 58 153aa long hypothetical protein #3 PH1834 300 111aa long hypothetical protein #4 PH1904 90 106aa long hypothetical protein Motif number 1 ATTCCCCCAGAGAGATATTGAAAAACATACCATC 1 104 0 AGAGTATAAA 0.84346 -197 TATCTCTCTGGGGGAATCGTGAGGAGAGCTACTT 1 121 1 GGGGATGAGG 0.773286 -180 AATCGTGAGGAGAGCTACTTCAAAAATTTATATT 1 135 1 AGAGTATAAA 0.84346 -166 ATGTTTTCGAAGAGAAAATATAAATTTTTGAAGT 1 151 0 AGAGAATAAA 0.943766 -150 CTGGAAGCTTGGAGCAATTGAAAGCTAACACTAG 1 222 1 GGAGAATAAG 0.977292 -79 GATAAATTTTGAAGAAAAGGCAAAATACTAGTGT 1 249 0 GAAGAAGAAA 0.947898 -52 ATAGCAAGGAGTAGCAACGTCAGAATAGTTATAG 3 33 0 GTAGAAGAGA 0.83893 -268 GGCTTTCAAAGGAGCTTTGGGAAATAGCAAGGAG 3 56 0 GGAGTTGAAA 0.931018 -245 TCCTAAGGCCAGAGAAAGGGAAGGTATTGAGCTC 3 127 0 AGAGAAGAGG 0.963986 -174 CAAAAATTTTAGAGAAAGCTAAAAATCCTAAGGC 3 152 0 AGAGAACAAA 0.883184 -149 ATGCGTAACGGGAGAATTGGGAAGGCCATTAACG 3 223 0 GGAGATGAAG 0.977189 -78 TTACTCCTCAGAAGTAATGCCAAGCCAGGAGACT 3 261 0 GAAGAAGAAG 0.94882 -40 TTGCTTTAGAGGATTAACGTTAAATTTTAGAGCA 4 35 0 GGATAAGAAA 0.8961 -56 **** ** * *** Masking position 12 Map Score: 11.1885 Number of sites scoring better than the average of aligned sites = 1298 Number in coding regions = 1203 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 TTCACACATGCCAAAGTAATAGATCATCCTGC 1 38 0 CCAAAGTAAG 0.946973 -263 TGTGAACTTTCTAAAGAAAATTGGAAATCTTT 1 64 1 CTAAAGAAAT 0.959614 -237 CACGATTCCCCCAGAGAGATATTGAAAAACAT 1 110 0 CCAGAGAGAT 0.895412 -191 CTCTGGAAGCTTGGAGCAATTGAAAGCTAACA 1 220 1 TTGGAGCAAG 0.915741 -81 GGGATAAATTTTGAAGAAAAGGCAAAATACTA 1 253 0 TTGAAGAAAG 0.874261 -48 AATCCTAAGGCCAGAGAAAGGGAAGGTATTGA 3 131 0 CCAGAGAAAG 0.984955 -170 ACCAAAAATTTTAGAGAAAGCTAAAAATCCTA 3 156 0 TTAGAGAAAT 0.94176 -145 CTCCCTTTAACCAAAGTAAAAGGGCCGTTAAT 3 198 1 CCAAAGTAAG 0.946974 -103 ACGTTAAATTTTAGAGCAACCTAACTATTCGA 4 21 0 TTAGAGCAAT 0.940652 -70 CGTTAATCCTCTAAAGCAATTTTTAAATAGCC 4 50 1 CTAAAGCAAT 0.95883 -41 ********* * Masking position 5 Map Score: 7.34118 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 269 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 3 TAAAGAAAATTGGAAATCTTTGCTACGCTGATGG 1 75 1 TGATCTTGCT 0.99245 -226 AAAGGCAAAATACTAGTGTTAGCTTTCAATTGCT 1 234 0 TAATGTTGCT 0.985982 -67 AATATTAGCTTGAAAATGTTGACTATCGT 2 6 0 TGATGTTACT 0.885134 -53 ATTTCCAATTTATAAATATTAGCTTGAAAATGTT 2 20 0 TAATATTGCT 0.962624 -39 ATTCTGACGTTGCTACTCCTTGCTATTTCCCAAA 3 41 1 TGATCCTGCT 0.986741 -260 TCTCTGGCCTTAGGATTTTTAGCTTTCTCTAAAA 3 146 1 TAATTTTGCT 0.962712 -155 TTACGCATACTAAGTCTCCTGGCTTGGCATTACT 3 249 1 TATTCCTGCT 0.965435 -52 CGAAAACTCTATTTTTCTTGGCTATTTAAAAAT 4 68 0 TATTCTTGCT 0.980129 -23 ** * **** *** Masking position 7 Map Score: 7.76657 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 72 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 GCAATGGGGCAAGTAGCTCTCTTGCC 1 6 0 AGTAGCTCTC 0.989359 -295 TAAATTTTTGAAGTAGCTCTCCTCACGATTC 1 134 0 AGTAGCTCTC 0.989359 -167 CCAAGCTTCCAGAGAGCACTCCAAGTGATCT 1 203 0 AAGAGCACTC 0.921447 -98 AAAATACTAGTGTTAGCTTTCAATTGCTCCA 1 231 0 TTTAGCTTTC 0.93173 -70 CGGGCTTTCAAAGGAGCTTTGGGAAATAGCA 3 61 0 AGGAGCTTTG 0.938984 -240 AAGGGAAGGTATTGAGCTCTCAAACTATGCG 3 115 0 ATGAGCTCTC 0.989451 -186 GCCTTAGGATTTTTAGCTTTCTCTAAAATTT 3 152 1 TTTAGCTTTC 0.93173 -149 GCCAAGAAAAATAGAGTTTTCG 4 79 1 AAGAGTTTTC 0.821693 -12 * ********* Masking position 5 Map Score: 8.21172 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 233 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 AAAATTTATATTTTCTCTTCGAAAACATCA 1 157 1 TTTTCTCTTC 0.912977 -144 TTTACTGGTATTTTATCCTCATCTATAACT 3 11 1 TTTTATCCTC 0.958185 -290 CTATTCTGACGTTGCTACTCCTTGCTATTT 3 39 1 GTTGCTACTC 0.944969 -262 TTTTGGTGGGATTTCTTCTCCCTTTAACCA 3 181 1 ATTTCTTCTC 0.880519 -120 GAGGGAGTAGGTTACTCCTCAGAAGTAATG 3 276 0 GTTACTCCTC 0.990708 -25 AAAATTTAACGTTAATCCTCTAAAGCAATT 4 41 1 GTTAATCCTC 0.972972 -50 ********** Masking position 6 Map Score: 2.8182 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 339 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 GGGGCAAGTAGCTCTCTTGCC 1 2 0 GCTCTCTTGC 0.982516 -299 AGAGCTACTTGCCCCATTGCCGCAGGATGA 1 17 1 GCCCCATTGC 0.940838 -284 GCCGCAGGATGATCTATTACTTTGGCATGT 1 35 1 GATCTATTAC 0.796611 -266 AAGGTATTGAGCTCTCAAACTATGCGAACT 3 111 0 GCTCTCAAAC 0.860018 -190 GGATTTCTTCTCCCTTTAACCAAAGTAAAA 3 189 1 TCCCTTTAAC 0.88097 -112 GCCATTAACGGCCCTTTTACTTTGGTTAAA 3 203 0 GCCCTTTTAC 0.984218 -98 AGTAACCTACTCCCTCTTCCT 3 290 1 TCCCTCTTCC 0.94526 -11 ********** Masking position 4 Map Score: 0.854932 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 378 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 ********** No masking Map Score: -1.51102e-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 8 ********** No masking Map Score: -1.51102e-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 9 ********** No masking Map Score: -1.51102e-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