AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -inarL_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 PH0514 300 352aa long hypothetical protein #3 PH0538 78 290aa long hypothetical protein #4 PH1359 300 639aa long hypothetical protein #5 PH1509 300 440aa long hypothetical NADH oxidase #6 PH1670 300 102aa long hypothetical protein Motif number 1 GCAATGGGGCAAGTAGCTCTCTTGCC 1 5 0 AGTAGCTCCT 0.873299 -296 TAAATTTTTGAAGTAGCTCTCCTCACGATTCC 1 133 0 AGTAGCTCCC 0.971927 -168 ACTCCAAGTGATCTACCTCGCCCTGAAGGGTG 1 185 0 ACTACCTCCC 0.981896 -116 AAGGGCTAGTAATTTACTCACCACTTTTCTCA 2 231 1 ATTTACTCCC 0.921895 -70 TTTACTCACCACTTTTCTCACCCCTCAAGGAA 2 243 1 ATTTTCTCCC 0.974896 -58 CCTTTTCAAAATCTTCCTCGCTTTCCAAGATC 4 248 0 ACTTCCTCCT 0.958889 -53 ATATTTTACAACGTACCTCCCCTTTTCAAAAT 4 268 0 AGTACCTCCC 0.985333 -33 CGAATGCCCTCATTTTCTCCCCAACATTTTAA 5 244 1 CTTTTCTCCC 0.918514 -57 TATCTCTTAACCCTTTCTCTCTTGGGTGGAGA 5 276 1 CCTTTCTCCT 0.742878 -25 TTTTCTCTAGAGGTTTCTCCCCTAATTATCTC 6 19 1 AGTTTCTCCC 0.984109 -282 GGAACTTATAAAGTTCCTCTCAAAGATTCTTG 6 62 0 AGTTCCTCCA 0.919576 -239 TAAGTTCCTTATTTGCCTCCCCTTTAACTGGA 6 86 1 ATTGCCTCCC 0.949944 -215 AACTCCTTCAATCTTGTTCTCCTTGGAGTTTG 6 159 1 ACTTGTTCCC 0.786104 -142 TTCCTTAAGCACTTTCCTCACCCAATATCTTT 6 228 1 ATTTCCTCCC 0.98913 -73 * ******* ** Masking position 8 Map Score: 21.069 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 329 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 ATCAGCGTAGCAAAGATTTCCAATTTTCTTTAGAAAGTTCAC 1 65 0 CTTTTTTTTA 0.891135 -236 AGAGCTACTTCAAAAATTTATATTTTCTCTTCGAAAACATCA 1 145 1 CTTTTTCTTC 0.974542 -156 AAAGCTAACACTAGTATTTTGCCTTTTCTTCAAAATTTATCC 1 242 1 CTTTTTTTCA 0.9476 -59 TAATCTATAGCTCGCGCTTTCAATATCCATCCTTGCGAACTT 2 90 1 CTTTATCTCC 0.983983 -211 ATAACTCTCTCAAGCTTTTCCATTTTTAATCTCCTCCTAAAT 4 29 0 CTTTTTTTCT 0.877408 -272 CAGAAGCTACCCGTAAATTCTATTATCACTTCATCATCTGAA 4 125 0 CTTTATCTTC 0.965286 -176 TCCAAGATCTCAACTGGTTTTATTTTTAATCCGAAATCCAAG 4 215 0 CTTTTTTTCC 0.986488 -86 CAAATGTTGACATTTTGTTGGCCTTTCCTTCCTTATTTCGAT 5 116 0 CTTTTTCTCC 0.988314 -185 AAAATGAGGGCATTCGTTCAAATTTTTCCTTCATATTTCAGT 5 218 0 CTCTTTTTTC 0.850142 -83 TCATTTTCTCCCCAACATTTTAATATCTCTTAACCCTTTCTC 5 253 1 CTTTATCTTA 0.873224 -48 AGCTTTTATGCTTATCCTTATTCTATTTTTCCAATTGTCAAC 6 120 1 CTTTATTTCC 0.981492 -181 TTTGGTCTGACTATTACTTGAATTATTGTTCCATCTTTGGTT 6 187 1 CTTTATTTCC 0.981492 -114 * ** **** *** Masking position 14 Map Score: 13.315 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 189 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 CTAAAGAAAATTGGAAATCTTTGCTACGCTGATG 1 74 1 TTATCTTTGC 0.956118 -227 CAATCCAAAGTCGTCAAGCTTTCCTAATCTATAG 2 66 1 TCAGCTTTCC 0.784734 -235 AATATCCATCCTTGCGAACTTTGCTATCTCCTCA 2 111 1 CTAACTTTGC 0.862376 -190 GAAGTCTATATCCTTAAGCTTTGGATAAGCTTCA 2 198 1 TCAGCTTTGG 0.935076 -103 CAAGGAAACGTTAAATATCTTTGGGGACTATATT 2 268 1 TTATCTTTGG 0.916244 -33 CTTGATAACTCTCTCAAGCTTTTCCATTTTTAAT 4 41 0 CTAGCTTTTC 0.932824 -260 ATCTGAAAAGCGTAATATCTTTGCCTGGGCCTCA 4 98 0 CGATCTTTGC 0.961368 -203 TCATAGCGAGCTTCTCAGCTTTTCGGGAGTCAAT 5 30 0 CTAGCTTTTC 0.932824 -271 ATGTCAACATTTGGAGATCTTTGCGCGATAAAGA 5 145 1 TTATCTTTGC 0.956117 -156 GACTTTTGCCCCAAGAATCTTTGAGAGGAACTTT 6 51 1 CCATCTTTGA 0.833123 -250 CCCCTTTAACTGGAGGAGCTTTTATGCTTATCCT 6 104 1 TGAGCTTTTA 0.515747 -197 CTTGAATTATTGTTCCATCTTTGGTTTCCTTAAG 6 203 1 TGATCTTTGG 0.888102 -98 ACTTTCCTCACCCAATATCTTTTCTACGAACCAC 6 238 1 CCATCTTTTC 0.903837 -63 GGTATTAAATCTTCGTAGCCTTGGCCA 6 284 1 CTAGCCTTGG 0.782857 -17 ** ******** Masking position 7 Map Score: 10.6415 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 397 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TGAAGTAGCTCTCCTCACGATTCCCCCAGAGAGATATT 1 119 0 CTCTCACGCA 0.980739 -182 TTGGAGTGCTCTCTGGAAGCTTGGAGCAATTGAAAGCT 1 210 1 CTCGGAAGCA 0.970746 -91 CATGTCACTTCTCCTCACGACCAATCCAAAGTCGTCAA 2 45 1 CTCTCACGCA 0.980739 -256 CCAATCCAAAGTCGTCAAGCTTTCCTAATCTATAGCTC 2 65 1 GTCTCAAGAA 0.86862 -236 ACTTTGCTATCTCCTCAAGGGGAACCCACCTATAGTAC 2 128 1 CTCTCAAGCA 0.992519 -173 AAATTACTAGCCCTTGAAGCTTATCCAAAGCTTAAGGA 2 208 0 CCCTGAAGAA 0.977914 -93 ACTTTTCTCACCCCTCAAGGAAACGTTAAATATCTTTG 2 253 1 CCCTCAAGTA 0.958495 -48 CCCTGCAAGTTACTTGCACCCCCACAAG 3 1 1 CCCGCAAGCA 0.987106 -78 TTACTTGCACCCCCACAAGTTAAAACCATTTCCAAAAC 3 20 1 CCCACAAGCA 0.965596 -59 GGGCCTCACTCCCATGAAGTCTGTTAAATTCCTTGATA 4 68 0 CCCTGAAGAA 0.977914 -233 CGGAGAGATGCTCCTGAACTCTAGACAAAAAACTCACT 5 183 1 CTCTGAACAA 0.793944 -118 *** ***** ** Masking position 7 Map Score: 10.3147 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 175 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 CTTTCTAAAGAAAATTGGAAATCTTTGCTA 1 70 1 AAAATTGGAA 0.839846 -231 TCCCCCAGAGAGATATTGAAAAACATACCA 1 106 0 AGATATTGAA 0.922748 -195 AGAAAATATAAATTTTTGAAGTAGCTCTCC 1 143 0 AATTTTTGAA 0.629795 -158 GTATTGGGATAAATTTTGAAGAAAAGGCAA 1 260 0 AAATTTTGAA 0.907426 -41 CGCGAGCTATAGATTAGGAAAGCTTGACGA 2 76 0 AGATTAGGAA 0.928713 -225 TCGCAAGGATGGATATTGAAAGCGCGAGCT 2 98 0 GGATATTGAA 0.618414 -203 GTAGAGCTGAAGATGAGGTACTATAGGTGG 2 153 0 AGATGAGGTA 0.36827 -148 ACTTTATAAGAGTTTTGGAAATGGTTTTAA 3 39 0 AGTTTTGGAA 0.814472 -40 GGAGGAGATTAAAAATGGAAAAGCTTGAGA 4 34 1 AAAAATGGAA 0.819058 -267 TACGCTTTTCAGATGATGAAGTGATAATAG 4 118 1 AGATGATGAA 0.776965 -183 AAAGCGAGGAAGATTTTGAAAAGGGGAGGT 4 256 1 AGATTTTGAA 0.932603 -45 AGGTTTATCGAAATAAGGAAGGAAAGGCCA 5 110 1 AAATAAGGAA 0.888469 -191 ATATGAAGGAAAAATTTGAACGAATGCCCT 5 224 1 AAAATTTGAA 0.741517 -77 AAGGGGAGGCAAATAAGGAACTTATAAAGT 6 80 0 AAATAAGGAA 0.888469 -221 TAAGGAAACCAAAGATGGAACAATAATTCA 6 205 0 AAAGATGGAA 0.726419 -96 ********** Masking position 10 Map Score: 10.5654 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 658 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 CAATTTTCTTTAGAAAGTTCACACATGCCAAAGT 1 53 0 TGAAGTTCCC 0.958142 -248 GTAGATCACTTGGAGTGCTCTCTGGAAGCTTGGA 1 201 1 TGATGCTCCG 0.953914 -100 CTTGGAGCAATTGAAAGCTAACACTAGTATTTTG 1 229 1 TGAAGCTACC 0.988027 -72 GCTTTCCTAATCTATAGCTCGCGCTTTCAATATC 2 83 1 TTAAGCTCCC 0.964643 -218 AAGTGGTGAGTAAATTACTAGCCCTTGAAGCTTA 2 223 0 TAATACTACC 0.735259 -78 GTTAAATTCCTTGATAACTCTCTCAAGCTTTTCC 4 50 0 TGAAACTCCC 0.965936 -251 CCTCTCCTTATCGAATGCTAGCTCATACTGCTTT 5 79 0 TGATGCTACC 0.985014 -222 * ** ***** * * Masking position 4 Map Score: 0.991082 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 93 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 TTCAATATCTCTCTGGGGGAATCGTGAGGA 1 116 1 CTCTGGGGGA 0.950657 -185 AGGTAGATCACTTGGAGTGCTCTCTGGAAG 1 199 1 CTTGGAGTGC 0.765205 -102 TCTCTGGAAGCTTGGAGCAATTGAAAGCTA 1 219 1 CTTGGAGCAA 0.881997 -82 CGTTAAATATCTTTGGGGACTATATTAATA 2 276 1 CTTTGGGGAC 0.919179 -25 ATGGTTTTAACTTGTGGGGGTGCAAGTAAC 3 19 0 CTTGTGGGGG 0.857912 -60 AGCTTCTCAGCTTTTCGGGAGTCAATCCTC 5 26 0 CTTTTCGGGA 0.857451 -275 GAGAAGCTCGCTATGAGGGATGATAATGGA 5 48 1 CTATGAGGGA 0.83556 -253 ATTTGGAGATCTTTGCGCGATAAAGATAAT 5 153 1 CTTTGCGCGA 0.947179 -148 CCCTTTCTCTCTTGGGTGGAGATGC 5 286 1 CTTGGGTGGA 0.919929 -15 CTCAAAGATTCTTGGGGCAAAAGTCGAGAT 6 46 0 CTTGGGGCAA 0.950302 -255 ********** Masking position 2 Map Score: 2.36013 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 448 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 TAGATCATCCTGCGGCAATGGGGCAAGTAGC 1 20 0 TGCGGCAATG 0.986559 -281 AATATCTCTCTGGGGGAATCGTGAGGAGAGC 1 119 1 TGGGGGAATG 0.986559 -182 TCTGGAAGCTTGGAGCAATTGAAAGCTAACA 1 221 1 TGGAGCAATG 0.980207 -80 CAAAGATTCTTGGGGCAAAAGTCGAGATAAT 6 43 0 TGGGGCAAAG 0.987321 -258 ********* * Masking position 7 Map Score: 0.248788 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 14 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 ********** No masking Map Score: 3.00803e-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: 3.00803e-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: 3.00803e-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