AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ipdhR_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 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 TTCTCCAATGTCCATAACTCACCCTAAGTT 1 14 0 TCCATAACTC 0.902128 -86 TTAAAGTACCTCCCTATCTAGCAACCCAAG 3 46 1 TCCCTATCTA 0.987318 -255 GCAACCCAAGTTCCTCACCATCTTCCCTAA 3 66 1 TTCCTCACCA 0.883029 -235 CTCACCATCTTCCCTAACTCTGATCCTACC 3 79 1 TCCCTAACTC 0.989476 -222 TATTGAAATATCCTTAACTGGAGTTAAGAC 3 127 1 TCCTTAACTG 0.858419 -174 CTTCAAGCCTCCCCTCACTAAAATTTATAG 3 156 1 CCCCTCACTA 0.966451 -145 ACAAAAACCTTCCTTATCTAGCAAACCTAG 3 208 1 TCCTTATCTA 0.930827 -93 CAACCCTCGGTCCCTCACTT 3 291 1 TCCCTCACTT 0.969473 -10 CTTCCCTCCCCCAAGAAGTTAC 4 3 1 TCCCTCCCCC 0.9605 -98 TCTGATCCCTCTCCATCCCTGCTAT 4 86 0 TCCCTCTCCA 0.984949 -15 TAGTTTAAAATCCCTATGTAATAGGGATTT 6 58 1 TCCCTATGTA 0.900876 -32 ********** Masking position 5 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 0.976727 -99 CTCTTCTTTCCTTTAAAGTTTATATTCCTATT 2 15 1 CTTAAATTTA 0.915769 -48 TAATACTTAAGCAAAAGGTTTATTAAATATAT 3 17 0 GCAAAGTTTA 0.799117 -284 TAGGGAGGTACTTTAATACTTAAGCAAAAGGT 3 30 0 CTTAATCTTA 0.886619 -271 TGAGGGGAGGCTTGAAGTCTTAACTCCAGTTA 3 141 0 CTGAAGCTTA 0.950713 -160 ATACTCAAGGCTATAAATTTTAGTGAGGGGAG 3 164 0 CTTAAATTTA 0.915769 -137 AGGTACTAAACCGAAATACTTAACATCTATTG 4 35 0 CCAAATCTTA 0.925763 -66 CGGTTTAGTACCTAAAGACTTAATAAGGGGAA 4 54 1 CCAAAGCTTA 0.978593 -47 TTGTCCGAATCATGAAACCTTAAATGATTTAA 5 57 1 CAGAAACTTA 0.840308 -78 GATTTAAAAACCTTGAGGTTTAACTATTTCAA 5 82 1 CCTGAGTTTA 0.887682 -53 CTATTTTATTCAAAAAATTTTATAATGTTCCC 6 29 0 CAAAAATTTA 0.825441 -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 GGTGAGTTATGGACATTGGAGAACTAAGGTA 1 21 1 GGACATGGAG 0.993548 -79 TATCAATTTCGGAAATTCGAGCCTGGAG 1 82 1 GGAAATCGAG 0.977059 -18 AAACTTTAAAGGAAAGAAGAGAGCT 2 5 0 GGAAAGAGAG 0.928291 -58 TCAGAGTTAGGGAAGATGGTGAGGAACTTGG 3 71 0 GGAAGAGGTG 0.932923 -230 CTTAATAAGGGGAAATAGCAGGGATGGAGAG 4 72 1 GGAAATGCAG 0.97276 -29 TGATGAGAGTGGAGGTGGGAGGAA 5 4 0 GGAGGTGGAG 0.982551 -131 TTCATGATTCGGACAAGGGAAACCCCGATGA 5 42 0 GGACAAGGAA 0.914572 -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 4 GGTTTCATATATTTAATAAACCTTTTGCTTAA 3 11 1 ATTTAAAACC 0.97248 -290 TTGCTTAAGTATTAAAGTACCTCCCTATCTAG 3 35 1 ATTAAATACT 0.680014 -266 GTACCTCCCTATCTAGCAACCCAAGTTCCTCA 3 51 1 ATCTAGAACC 0.98213 -250 CTCTGTGATTATTGAAATATCCTTAACTGGAG 3 118 1 ATTGAATACC 0.936825 -183 AACCTTCCTTATCTAGCAAACCTAGAAGTAAA 3 213 1 ATCTAGAACC 0.982113 -88 CTTAACATCTATTGAGGTAACTTCTTGGGGGA 4 17 0 ATTGAGTACT 0.901884 -84 ACCTTAAATGATTTAAAAACCTTGAGGTTTAA 5 73 1 ATTTAAAACT 0.932518 -62 GCTGTCACCTAGAAATCCCTATTACATA 6 72 0 ACCTAGAACC 0.935892 -18 ****** ** ** Masking position 5 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 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 TTGCTAGATAGGGAGGTACTTTAATACTTA 3 40 0 GGGAGGTACT 0.963073 -261 TTTTAGTGAGGGGAGGCTTGAAGTCTTAAC 3 149 0 GGGAGGCTTG 0.97108 -152 TGCTAGATAAGGAAGGTTTTTGTCAAGGAG 3 201 0 GGAAGGTTTT 0.852228 -100 AACTTCTTGGGGGAGGGAAG 4 1 0 GGGAGGGAAG 0.97108 -100 CTGATGAGAGTGGAGGTGGGAGGAA 5 6 0 TGGAGGTGGG 0.928006 -129 CATTCAAACTGGGAGGTGATTGC 5 122 1 GGGAGGTGAT 0.985668 -13 CCAAAGATCAAGGAGGTTAG 6 1 0 AGGAGGTTAG 0.953175 -89 ********** Masking position 4 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 0.924185 -29 ACCTAGAAGTAAATTGCTAAGCTTAGAAAA 3 232 1 AAATTGCTAA 0.947556 -69 TACTAAACCGAAATACTTAACATCTATTGA 4 34 0 AAATACTTAA 0.926119 -67 GACAATCTTGAAATAGTTAAACCTCAAGGT 5 91 0 AAATAGTTAA 0.977845 -44 TTTTTGAATAAAATAGTTTAAAATCCCTAT 6 45 1 AAATAGTTTA 0.930625 -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