AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -irpoE_tpal_opreg_300.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0091 181 cysteinyl-tRNA synthetase (cysS) #2 TP0092 70 RNA polymerase sigma-24 factor (rpoE) #3 TP0773 300 periplasmic serine protease DO (htrA-1) #4 TP0841 300 periplasmic serine protease DO (htrA-2) Motif number 1 GCGCGACAATGGGGCTGGGCGTGGTCCGCA 1 120 1 GGGGCTGGGC 0.948832 -62 AAATCTGCATCATCCTGTGCTCTTAAAAGC 2 44 0 CATCCTGTGC 0.939184 -27 GTGCCTTCACCGGCGTGGGAGTTCAAGTC 3 10 0 CGGCGTGGGA 0.984998 -291 AAAACCCTTCCATGGTGGGAAATATAGTTT 3 86 1 CATGGTGGGA 0.978268 -215 GCCGCCTTTGCATCCCGTGCCCTGAAAGCT 3 137 0 CATCCCGTGC 0.896195 -164 CCACGCGCAGCGCCGCGGGCAGCGTGTATT 3 190 0 CGCCGCGGGC 0.994972 -111 CTGCGCGTGGCGCCGTGGGCTATTAGCTCA 3 210 1 CGCCGTGGGC 0.997226 -91 AAGTGTGCGCGGTGTGCTGATAGTACA 4 8 1 CGCGGTGTGC 0.995109 -293 GCTGATAGTACATGCAGGGAGCAGTTTGTG 4 26 1 CATGCAGGGA 0.915111 -275 GCAGTTTGTGCACGGTAGGCAGCGTGTAAG 4 46 1 CACGGTAGGC 0.920076 -255 TGTAAGTGTACGTGGCGGGCACAGGTGAAG 4 70 1 CGTGGCGGGC 0.995526 -231 GTAACCATATCGCTGTGTGCTGCTTTTAAC 4 113 1 CGCTGTGTGC 0.946738 -188 GCTTTTAACCCGGGCTGTGTCGGTAGGGGT 4 134 1 CGGGCTGTGT 0.860531 -167 GGTTTGGGTACGCGCAGGGACGTGGAGGGA 4 161 1 CGCGCAGGGA 0.981826 -140 CGCGCAGGGACGTGGAGGGACTCATGAACA 4 171 1 CGTGGAGGGA 0.980435 -130 ********** Masking position 9 Map Score: 28.9205 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 852 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 GCTTATGCTACAATGGCGCGGTCTTGGCCTT 1 38 1 CAATGGCGCG 0.956522 -144 GACTGAAGCGCAGGCGGGCAAAGGCGTTTGC 1 91 1 CAGGCGGGCA 0.757484 -91 GTTTGCGCGACAATGGGGCTGGGCGTGGTCC 1 116 1 CAATGGGGCG 0.904675 -66 GTTTCTCCCAACCGGGCGCAGAACACGTGCG 1 146 0 ACCGGGCGCG 0.97806 -36 AGAAACTTCGAAGGGGCGCAC 1 171 1 AAGGGGCGCC 0.976128 -11 CTAGTGCCTTCACCGGCGTGGGAGTTCAAGT 3 12 0 CACCGGCGTG 0.948177 -289 CGGGATGCAAAGGCGGCGTACTTGACAAAAT 3 150 1 AGGCGGCGTC 0.807061 -151 TACACGCTGCCCGCGGCGCTGCGCGTGGCGC 3 192 1 CCGCGGCGCG 0.5443 -109 AGCTAATAGCCCACGGCGCCACGCGCAGCGC 3 207 0 CCACGGCGCA 0.945616 -94 CCACGCCTTAAAAGGGCGTTGCTCTACCAGC 3 240 0 AAAGGGCGTG 0.956153 -61 TACTATCAGCACACCGCGCACACTT 4 5 0 ACACCGCGCC 0.861775 -296 TGCTGCTTTTAACCCGGGCTGTGTCGGTAGG 4 130 1 AACCCGGGCG 0.87222 -171 TGGGTACGCGCAGGGACGTGGAGGGACTCAT 4 165 1 CAGGGACGTG 0.822666 -136 TTTTTTACAGCAGCGGCGTTGCTCGTTTTTA 4 248 1 CAGCGGCGTG 0.576912 -53 ********* * Masking position 8 Map Score: 19.236 Number of sites scoring better than the average of aligned sites = 1688 Number in coding regions = 1544 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 3 GTAGACTGAAGCGCAGGCGGGCAAAGGCGT 1 88 1 GCGCAGGCGG 0.974135 -94 CACGTGCGGACCACGCCCAGCCCCATTGTC 1 124 0 CCACGCCCAG 0.89304 -58 CGGGCGCAGAACACGTGCGGACCACGCCCA 1 135 0 ACACGTGCGG 0.948141 -47 CGCACGTGTTCTGCGCCCGGTTGGGAGAAA 1 146 1 CTGCGCCCGG 0.68355 -36 GCTTTTAAGAGCACAGGATGATGCAGATTT 2 44 1 GCACAGGATG 0.71488 -27 GGCACGGGATGCAAAGGCGGCGTACTTGAC 3 146 1 GCAAAGGCGG 0.864078 -155 GCCAATTCCAATACACGCTGCCCGCGGCGC 3 181 1 ATACACGCTG 0.925491 -120 GCCCACGGCGCCACGCGCAGCGCCGCGGGC 3 200 0 CCACGCGCAG 0.728537 -101 AAGTGTGCGCGGTGTGCTGATA 4 3 1 GTGTGCGCGG 0.841886 -298 TGTGCTGATAGTACATGCAGGGAGCAGTTT 4 23 1 GTACATGCAG 0.925028 -278 CCACGTACACTTACACGCTGCCTACCGTGC 4 55 0 TTACACGCTG 0.831003 -246 GCTGCTTTTAACCCGGGCTGTGTCGGTAGG 4 131 1 ACCCGGGCTG 0.778379 -170 AGGGGTTTGGGTACGCGCAGGGACGTGGAG 4 158 1 GTACGCGCAG 0.983057 -143 TGTGTGTGGGGTACATGCGGTATGCCGCAG 4 217 1 GTACATGCGG 0.965968 -84 ********** Masking position 10 Map Score: 13.6422 Number of sites scoring better than the average of aligned sites = 3094 Number in coding regions = 2857 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 4 CCCCATTGTCGCGCAAACGCCTTTGCCCGCCT 1 102 0 GCCAAACCCT 0.995718 -80 TGCGGACCACGCCCAGCCCCATTGTCGCGCAA 1 118 0 GCCAGCCCAT 0.908216 -64 GCCGGTGAAGGCACTAGCACCTGAAGCTAGCG 3 26 1 GCCTAGCCCT 0.988376 -275 CCTGAAAGCTGCTCTAATCCCTTGACTAGAAA 3 115 0 GCCTAATCCT 0.967911 -186 TGCATCCCGTGCCCTGAAAGCTGCTCTAATCC 3 127 0 GCCTGAAGCT 0.913032 -174 AAAGGGCGTTGCTCTACCAGCTGAGCTAATAG 3 229 0 GCCTACCGCT 0.98971 -72 TGCCTACCGTGCACAAACTGCTCCCTGCATGT 4 35 0 GCCAAACGCT 0.993052 -266 CCCTGCGCGTACCCAAACCCCTACCGACACAG 4 148 0 ACCAAACCCT 0.962919 -153 ** ***** *** Masking position 12 Map Score: 9.67394 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 212 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 ACGATTTCACGCGCTTATGCTACAATGGCG 1 26 1 GCGCTTATGC 0.970403 -156 TTGCCCGCCTGCGCTTCAGTCTACCCTCCC 1 82 0 GCGCTTCAGT 0.811596 -100 GCGGGCAAAGGCGTTTGCGCGACAATGGGG 1 104 1 GCGTTTGCGC 0.899391 -78 ATGAGCAGGAGCTTTTAAGAGCACAGGATG 2 34 1 GCTTTTAAGA 0.718695 -37 GGATGATGCAGATTTTAAGCTC 2 59 1 GATTTTAAGC 0.800246 -12 CCTGAAGCTAGCGTGTCTGCCAATTCCACC 3 45 1 GCGTGTCTGC 0.958247 -256 ACGGTAGGCAGCGTGTAAGTGTACGTGGCG 4 57 1 GCGTGTAAGT 0.936868 -244 ATATGGTTACGAGTTTATCCCCTCTTCACC 4 93 0 GAGTTTATCC 0.838141 -208 GCTGTGTGCTGCTTTTAACCCGGGCTGTGT 4 124 1 GCTTTTAACC 0.93774 -177 CCACGTCCCTGCGCGTACCCAAACCCCTAC 4 156 0 GCGCGTACCC 0.968217 -145 GCGGCATACCGCATGTACCCCACACACAAA 4 215 0 GCATGTACCC 0.84545 -86 ********** Masking position 6 Map Score: 6.43812 Number of sites scoring better than the average of aligned sites = 1221 Number in coding regions = 1134 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 TCTTTGCGTTTCGAGGGAGGGTAGACTGAA 1 68 1 TCGAGGGAGG 0.949203 -114 CGTTTGCGCGACAATGGGGCTGGGCGTGGT 1 115 1 ACAATGGGGC 0.859175 -67 GGGAGAAACTTCGAAGGGGCGCAC 1 168 1 TCGAAGGGGC 0.981914 -14 TTTTCTTGCCTCGATGGTGGAATTGGCAGA 3 60 0 TCGATGGTGG 0.994088 -241 AGAAAACCCTTCCATGGTGGGAAATATAGT 3 84 1 TCCATGGTGG 0.974716 -217 AAGGCGTGGGTCGATGGTTCGAATCCATCA 3 262 1 TCGATGGTTC 0.920258 -39 CCATCATGGCTCAGAGGTGGGATTG 3 286 1 TCAGAGGTGG 0.918693 -15 CCGGGCTGTGTCGGTAGGGGTTTGGGTACG 4 143 1 TCGGTAGGGG 0.927742 -158 ********** Masking position 7 Map Score: 6.4422 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 207 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CGCAAAGAAGGCCAAGACCGCGCCATTGTA 1 46 0 GCCAAGACCG 0.969085 -136 ACACGTGCGGACCACGCCCAGCCCCATTGT 1 125 0 ACCACGCCCA 0.963156 -57 TAGCGTGTCTGCCAATTCCACCATCGAGGC 3 53 1 GCCAATTCCA 0.977363 -248 TTGGCATTTTGTCAAGTACGCCGCCTTTGC 3 156 0 GTCAAGTACG 0.794686 -145 TTGACAAAATGCCAATTCCAATACACGCTG 3 171 1 GCCAATTCCA 0.977363 -130 AGCCCACGGCGCCACGCGCAGCGCCGCGGG 3 201 0 GCCACGCGCA 0.978745 -100 ACCTGTGCCCGCCACGTACACTTACACGCT 4 66 0 GCCACGTACA 0.987863 -235 CATGAGTCCCTCCACGTCCCTGCGCGTACC 4 167 0 TCCACGTCCC 0.93332 -134 ********** Masking position 4 Map Score: 6.96177 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 239 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GGTAGACTGAAGCGCAGGCGGGCAAAGGCG 1 87 1 AGCGCAGGCG 0.967588 -95 CATTGTTGCATGAGCAGGAGCTTTTAAGAG 2 25 1 TGAGCAGGAG 0.877535 -46 GGAGCTTTTAAGAGCACAGGATGATGCAGA 2 41 1 AGAGCACAGG 0.921716 -30 TCAAGGGATTAGAGCAGCTTTCAGGGCACG 3 122 1 AGAGCAGCTT 0.839373 -179 AGCAGCTTTCAGGGCACGGGATGCAAAGGC 3 134 1 AGGGCACGGG 0.94674 -167 CGCCACGCGCAGCGCCGCGGGCAGCGTGTA 3 192 0 AGCGCCGCGG 0.987491 -109 GTGGGCTATTAGCTCAGCTGGTAGAGCAAC 3 224 1 AGCTCAGCTG 0.764203 -77 CTCAGCTGGTAGAGCAACGCCCTTTTAAGG 3 236 1 AGAGCAACGC 0.863462 -65 GCCCGGGTTAAAAGCAGCACACAGCGATAT 4 119 0 AAAGCAGCAC 0.616747 -182 CCCTACCGACACAGCCCGGGTTAAAAGCAG 4 132 0 ACAGCCCGGG 0.837859 -169 GGTTTGGGTACGCGCAGGGACGTGGAGGGA 4 161 1 CGCGCAGGGA 0.730114 -140 CAGTTTTTTTACAGCAGCGGCGTTGCTCGT 4 244 1 ACAGCAGCGG 0.984913 -57 TTGGATGACCAGAGCAGCAGATAAAAACGA 4 270 0 AGAGCAGCAG 0.988467 -31 ********** Masking position 5 Map Score: 8.837 Number of sites scoring better than the average of aligned sites = 1271 Number in coding regions = 1195 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 9 ********** No masking Map Score: 1.48747e-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: 1.48747e-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: 1.48747e-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