AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iarcA_pyro_opreg_100.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 GATGGTATGTTTTTCAATATCTCTCTGGGGGAAT 1 104 1 TTTATACTCT 0.841819 -197 AAGTAGCTCTCCTCACGATTCCCCCAGAGAGATA 1 121 0 CCTCATCCCC 0.77111 -180 AATATAAATTTTTGAAGTAGCTCTCCTCACGATT 1 135 0 TTTATACTCT 0.841819 -166 ACTTCAAAAATTTATATTTTCTCTTCGAAAACAT 1 151 1 TTTATTCTCT 0.943106 -150 CTAGTGTTAGCTTTCAATTGCTCCAAGCTTCCAG 1 222 0 CTTATTCTCC 0.977016 -79 ACACTAGTATTTTGCCTTTTCTTCAAAATTTATC 1 249 1 TTTCTTCTTC 0.947284 -52 CTATAACTATTCTGACGTTGCTACTCCTTGCTAT 3 33 1 TCTCTTCTAC 0.837251 -268 CTCCTTGCTATTTCCCAAAGCTCCTTTGAAAGCC 3 56 1 TTTCAACTCC 0.930219 -245 GAGCTCAATACCTTCCCTTTCTCTGGCCTTAGGA 3 127 1 CCTCTTCTCT 0.963554 -174 GCCTTAGGATTTTTAGCTTTCTCTAAAATTTTTG 3 152 1 TTTGTTCTCT 0.881901 -149 CGTTAATGGCCTTCCCAATTCTCCCGTTACGCAT 3 223 1 CTTCATCTCC 0.976911 -78 AGTCTCCTGGCTTGGCATTACTTCTGAGGAGTAA 3 261 1 CTTCTTCTTC 0.948216 -40 TGCTCTAAAATTTAACGTTAATCCTCTAAAGCAA 4 35 1 TTTCTTATCC 0.894942 -56 *** * ** **** Masking position 3 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 CCATTGCCGCAGGATGATCTATTACTTTGGCATGTG 1 30 1 AGATCTATAT 0.955969 -271 CCAAGCTTCCAGAGAGCACTCCAAGTGATCTACCTC 1 198 0 AGCACTCAAT 0.972777 -103 AGCAATTGAAAGCTAACACTAGTATTTTGCCTTTTC 1 234 1 AGCACTATAT 0.931928 -67 CCAAATTAGTCATATTTAAAAGTATTGGGATAA 1 278 0 AGATTTAAAT 0.931552 -23 ACGATAAATAGTTTAATTTCCAATTTATAAATATT 2 34 0 AGATTTCAAT 0.918228 -25 CTGGTATTTTATCCTCATCTATAACTATTCTGACGT 3 15 1 ATATCTAAAT 0.932155 -286 AAGGGAAGGTATTGAGCTCTCAAACTATGCGAACTC 3 110 0 ATCTCTCAAT 0.956935 -191 TAGGATTTTTAGCTTTCTCTAAAATTTTTGGTGGGA 3 156 1 AGCTCTAAAT 0.992756 -145 TCGAATAGTTAGGTTGCTCTAAAATTTAACGTTAAT 4 21 1 AGCTCTAAAT 0.992757 -70 ** ***** ** * Masking position 10 Map Score: 7.78155 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 129 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 GGGGCAAGTAGCTCTCTTGCC 1 2 0 GCTCTCTTGC 0.988368 -299 TTTTTCAATATCTCTCTGGGGGAATCGTGA 1 113 1 TCTCTCTGGG 0.988368 -188 TTTTGAAGTAGCTCTCCTCACGATTCCCCC 1 130 0 GCTCTCCTCA 0.860268 -171 AAATTTATATTTTCTCTTCGAAAACATCAC 1 158 1 TTTCTCTTCG 0.954186 -143 CACTTGGAGTGCTCTCTGGAAGCTTGGAGC 1 207 1 GCTCTCTGGA 0.973658 -94 ATACCTTCCCTTTCTCTGGCCTTAGGATTT 3 134 1 TTTCTCTGGC 0.970772 -167 AGTAACCTACTCCCTCTTCCT 3 290 1 TCCCTCTTCC 0.934002 -11 GAAAACTCTATTTTTCTTGGCTATTTAAAA 4 70 0 TTTTTCTTGG 0.790968 -21 ********** Masking position 5 Map Score: 6.05474 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 366 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 GGCAATGGGGCAAGTAGCTCTCTTGCC 1 8 0 CAAGTAGCTC 0.977493 -293 CCCATTGCCGCAGGATGATCTATTACTTTG 1 29 1 CAGGATGATC 0.915293 -272 ATAAATTTTTGAAGTAGCTCTCCTCACGAT 1 136 0 GAAGTAGCTC 0.971315 -165 CCTTCAGGGCGAGGTAGATCACTTGGAGTG 1 188 1 GAGGTAGATC 0.971315 -113 GAAGAGGGAGTAGGTTACTCCTCAGAAGTA 3 279 0 TAGGTTACTC 0.927403 -22 CTCGAATAGTTAGGTTGCTCTAAAATTTAA 4 20 1 TAGGTTGCTC 0.987126 -71 ********** Masking position 2 Map Score: 5.02741 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 169 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 AACTTTCTAAAGAAAATTGGAAATCTTTGC 1 68 1 AGAAAATTGG 0.906115 -233 AGTGCTCTCTGGAAGCTTGGAGCAATTGAA 1 214 1 GGAAGCTTGG 0.978465 -87 GGCTTTCAAAGGAGCTTTGGGAAATAGCAA 3 60 0 GGAGCTTTGG 0.974194 -241 ATGCGTAACGGGAGAATTGGGAAGGCCATT 3 227 0 GGAGAATTGG 0.991265 -74 TGCCAAGCCAGGAGACTTAGTATGCGTAAC 3 248 0 GGAGACTTAG 0.971129 -53 ********** Masking position 7 Map Score: 2.36666 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 127 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 ATTGGAAATCTTTGCTACGCTGATGGTATG 1 83 1 TTTGCTACGC 0.912517 -218 AAAATTTATATTTTCTCTTCGAAAACATCA 1 157 1 TTTTCTCTTC 0.894108 -144 TTTACTGGTATTTTATCCTCATCTATAACT 3 11 1 TTTTATCCTC 0.948564 -290 CTATTCTGACGTTGCTACTCCTTGCTATTT 3 39 1 GTTGCTACTC 0.978186 -262 GAGGGAGTAGGTTACTCCTCAGAAGTAATG 3 276 0 GTTACTCCTC 0.988482 -25 AAAATTTAACGTTAATCCTCTAAAGCAATT 4 41 1 GTTAATCCTC 0.966656 -50 ********** Masking position 6 Map Score: 3.25332 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 315 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 TTCACACATGCCAAAGTAATAGATCATCCT 1 40 0 CCAAAGTAAT 0.98435 -261 TGTGAACTTTCTAAAGAAAATTGGAAATCT 1 64 1 CTAAAGAAAA 0.918242 -237 CTCCCTTTAACCAAAGTAAAAGGGCCGTTA 3 198 1 CCAAAGTAAA 0.977726 -103 GGTTACTCCTCAGAAGTAATGCCAAGCCAG 3 267 0 CAGAAGTAAT 0.912189 -34 CGTTAATCCTCTAAAGCAATTTTTAAATAG 4 50 1 CTAAAGCAAT 0.959762 -41 ********** Masking position 5 Map Score: 1.60451 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 45 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 TTCGAAAACATCACCCTTCAGGGCGAGGTA 1 174 1 TCACCCTTCA 0.981513 -127 TGGGATTTCTTCTCCCTTTAACCAAAGTAA 3 187 1 TCTCCCTTTA 0.991137 -114 CCTTCCCAATTCTCCCGTTACGCATACTAA 3 232 1 TCTCCCGTTA 0.989342 -69 ********** Masking position 10 Map Score: 0.515404 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 39 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 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 Motif number 10 ********** 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 11 ********** 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