AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ipdhR_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 PH0092 99 821aa long hypothetical phosphoenolpyruvate synthase #2 PH0093 62 247aa long hypothetical protein #3 PH0198 300 168aa long hypothetical protein #4 PH0583 100 318aa long hypothetical protein #5 PH0614 134 332aa long hypothetical protein #6 PH1150 89 236aa long hypothetical arylmalonate decarboxylase Motif number 1 AACTTAGGGTGAGTTATGGACATTGGAGAA 1 14 1 GAGTTATGGA 0.913196 -86 CTTGGGTTGCTAGATAGGGAGGTACTTTAA 3 46 0 TAGATAGGGA 0.988871 -255 TTAGGGAAGATGGTGAGGAACTTGGGTTGC 3 66 0 TGGTGAGGAA 0.896008 -235 GGTAGGATCAGAGTTAGGGAAGATGGTGAG 3 79 0 GAGTTAGGGA 0.990767 -222 GTCTTAACTCCAGTTAAGGATATTTCAATA 3 127 0 CAGTTAAGGA 0.873737 -174 CTATAAATTTTAGTGAGGGGAGGCTTGAAG 3 156 0 TAGTGAGGGG 0.970483 -145 CTAGGTTTGCTAGATAAGGAAGGTTTTTGT 3 208 0 TAGATAAGGA 0.938866 -93 AAGTGAGGGACCGAGGGTTG 3 291 0 AAGTGAGGGA 0.973152 -10 GTAACTTCTTGGGGGAGGGAAG 4 3 0 GGGGGAGGGA 0.965222 -98 ATAGCAGGGATGGAGAGGGATCAGA 4 86 1 TGGAGAGGGA 0.986788 -15 AAATCCCTATTACATAGGGATTTTAAACTA 6 58 0 TACATAGGGA 0.912062 -32 ********** Masking position 6 Map Score: 15.2795 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 636 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 CCATAACTCACCCTAAGTTTTA 1 1 0 CCTAAGTTTA 0.975787 -99 CTCTTCTTTCCTTTAAAGTTTATATTCCTATT 2 15 1 CTTAAATTTA 0.91259 -48 TAATACTTAAGCAAAAGGTTTATTAAATATAT 3 17 0 GCAAAGTTTA 0.792533 -284 TAGGGAGGTACTTTAATACTTAAGCAAAAGGT 3 30 0 CTTAATCTTA 0.882481 -271 TGAGGGGAGGCTTGAAGTCTTAACTCCAGTTA 3 141 0 CTGAAGCTTA 0.948779 -160 ATACTCAAGGCTATAAATTTTAGTGAGGGGAG 3 164 0 CTTAAATTTA 0.91259 -137 AGGTACTAAACCGAAATACTTAACATCTATTG 4 35 0 CCAAATCTTA 0.922929 -66 CGGTTTAGTACCTAAAGACTTAATAAGGGGAA 4 54 1 CCAAAGCTTA 0.977727 -47 TTGTCCGAATCATGAAACCTTAAATGATTTAA 5 57 1 CAGAAACTTA 0.834794 -78 GATTTAAAAACCTTGAGGTTTAACTATTTCAA 5 82 1 CCTGAGTTTA 0.883578 -53 CTATTTTATTCAAAAAATTTTATAATGTTCCC 6 29 0 CAAAAATTTA 0.819527 -61 ** **** **** Masking position 6 Map Score: 8.659 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 335 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 TTAAGCAAAAGGTTTATTAAATATATGAAACC 3 11 0 GGTTTTAAAT 0.970287 -290 CTAGATAGGGAGGTACTTTAATACTTAAGCAA 3 35 0 AGTATTTAAT 0.662583 -266 TGAGGAACTTGGGTTGCTAGATAGGGAGGTAC 3 51 0 GGTTCTAGAT 0.98069 -250 CTCCAGTTAAGGATATTTCAATAATCACAGAG 3 118 0 GGTATTCAAT 0.931985 -183 TTTACTTCTAGGTTTGCTAGATAAGGAAGGTT 3 213 0 GGTTCTAGAT 0.980674 -88 TCCCCCAAGAAGTTACCTCAATAGATGTTAAG 4 17 1 AGTACTCAAT 0.894671 -84 TTAAACCTCAAGGTTTTTAAATCATTTAAGGT 5 73 0 AGTTTTAAAT 0.927373 -62 TATGTAATAGGGATTTCTAGGTGACAGC 6 72 1 GGTTCTAGGT 0.930985 -18 ** ** ****** Masking position 8 Map Score: 3.72038 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 138 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 GGTGAGTTATGGACATTGGAGAACTAAGGTA 1 21 1 GGACATGGAG 0.993865 -79 TATCAATTTCGGAAATTCGAGCCTGGAG 1 82 1 GGAAATCGAG 0.978169 -18 AAACTTTAAAGGAAAGAAGAGAGCT 2 5 0 GGAAAGAGAG 0.931595 -58 TCAGAGTTAGGGAAGATGGTGAGGAACTTGG 3 71 0 GGAAGAGGTG 0.936028 -230 CTTAATAAGGGGAAATAGCAGGGATGGAGAG 4 72 1 GGAAATGCAG 0.974072 -29 TGATGAGAGTGGAGGTGGGAGGAA 5 4 0 GGAGGTGGAG 0.983399 -131 TTCATGATTCGGACAAGGGAAACCCCGATGA 5 42 0 GGACAAGGAA 0.918453 -93 ****** **** Masking position 3 Map Score: 3.55334 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 335 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 CTGCTTGCACCGAAGAAATATCCAAAA 2 46 0 CACCGAAGAA 0.970546 -17 CTTCCCTCCCCCAAGAAGTTACCTCAA 4 8 1 CCCCCAAGAA 0.984651 -93 CCCCGATGAATCCCGCTGATGAGAGTGGAG 5 21 0 TCCCGCTGAT 0.94361 -114 ACAAGGGAAACCCCGATGAATCCCGCTGAT 5 31 0 CCCCGATGAA 0.991735 -104 TTTATAATGTTCCCAAAGATCAAGGAGGTT 6 13 0 TCCCAAAGAT 0.930588 -77 ********** Masking position 9 Map Score: 1.58722 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 104 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 6 TAAGTATTAAAGTACCTCCCTATCTAGCAA 3 40 1 AGTACCTCCC 0.966184 -261 GTTAAGACTTCAAGCCTCCCCTCACTAAAA 3 149 1 CAAGCCTCCC 0.973535 -152 CTCCTTGACAAAAACCTTCCTTATCTAGCA 3 201 1 AAAACCTTCC 0.863354 -100 CTTCCCTCCCCCAAGAAGTT 4 1 1 CTTCCCTCCC 0.973535 -100 TTCCTCCCACCTCCACTCTCATCAG 5 6 1 CCCACCTCCA 0.933869 -129 GCAATCACCTCCCAGTTTGAATG 5 122 0 ATCACCTCCC 0.986902 -13 CTAACCTCCTTGATCTTTGG 6 1 1 CTAACCTCCT 0.957084 -89 ********** Masking position 7 Map Score: 3.30506 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 386 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 CGAATTTCCGAAATTGATAAAGGTGGATCA 1 71 0 AAATTGATAA 0.920851 -29 ACCTAGAAGTAAATTGCTAAGCTTAGAAAA 3 232 1 AAATTGCTAA 0.945189 -69 TACTAAACCGAAATACTTAACATCTATTGA 4 34 0 AAATACTTAA 0.922863 -67 GACAATCTTGAAATAGTTAAACCTCAAGGT 5 91 0 AAATAGTTAA 0.976811 -44 TTTTTGAATAAAATAGTTTAAAATCCCTAT 6 45 1 AAATAGTTTA 0.927552 -45 ********** Masking position 4 Map Score: 1.81512 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 49 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 ********** No masking Map Score: -6.37056e-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: -6.37056e-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: -6.37056e-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