AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icpxR_tpal_opreg_100.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 TP0363 300 chemotaxis histidine kinase (cheA) #2 TP0438 29 conserved hypothetical protein #3 TP0439 86 purine-binding chemotaxis protein (cheW-2) #4 TP0726 57 flagellar protein (flbD) #5 TP0727 70 flagellar hook protein (flgE) #6 TP0728 75 flagellar hook assembly scaffolding protein (flgD) #7 TP0773 300 periplasmic serine protease DO (htrA-1) #8 TP0841 300 periplasmic serine protease DO (htrA-2) #9 TP0949 275 membrane protein #10 TP1016 72 basic membrane protein (tpn39b) #11 TP1017 171 alanyl-tRNA synthetase (alaS) Motif number 1 GCAGCTTTCTACCCACGCGCGGTCGTCTTGGGT 1 34 0 ACCCCCGCGT 0.993144 -267 TCAAAACCAGACCCTCTCGCAGCTTTCTACCCA 1 52 0 ACCCCCGCGC 0.996935 -249 ATCCAAACGTAGACCCCCACCGCTCGGTAGAGG 1 94 1 AGACCCACGC 0.933612 -207 AGGAGTAGGACCAGTCCCGCGGCATACAAGGAG 1 124 1 CCAGCCGCGC 0.878001 -177 TTGTCAGGTCGGTTTCTCGCCCTCGGTGGTTAC 1 156 0 GGTTCCGCCT 0.649234 -145 CTCCGCCATGGCCCGCGCGCAGGTACGTTTGTC 1 184 0 GCCCCCGCGG 0.994243 -117 CAAAAGACCCCGCCACCCGCTGCATCCCTTGAC 1 239 0 CGCCCCGCGC 0.996921 -62 ACGGAGTGCAGGACACGCGCTTGACTGCAGCTG 3 34 1 GGACCCGCTG 0.876346 -53 TTCGTACAATCCCTCCTCTCAGCTGCAGTCAAG 3 53 0 CCCTCCTCGC 0.701428 -34 ATCCCCATCACGCCACCTGCCGCTTAAGATACA 4 30 0 CGCCCTGCGC 0.973602 -28 GTGTACGCTGACCCCCCTACAGGGTAGGCAAAA 6 24 0 ACCCCTACGG 0.65444 -52 GACTTGAACTCCCACGCCGGTGAAGGCACT 7 8 1 ACTCCCGCGG 0.97423 -293 ACGCCGGTGAAGGCACTAGCACCTGAAGCTAGC 7 24 1 AGGCCAGCCC 0.637114 -277 GAATTGGCAGACACGCTAGCTTCAGGTGCTAGT 7 38 0 ACACCAGCTC 0.587908 -263 TTCCAATACACGCTGCCCGCGGCGCTGCGCGTG 7 186 1 CGCTCCGCGC 0.987905 -115 TAGCCCACGGCGCCACGCGCAGCGCCGCGGGCA 7 199 0 CGCCCCGCGC 0.996921 -102 TTCGAACCATCGACCCACGCCTTAAAAGGGCGT 7 252 0 CGACCCGCTT 0.847347 -49 CGCCACGTACACTTACACGCTGCCTACCGTGCA 8 54 0 ACTTCCGCGC 0.94955 -247 CCGGGTTAAAAGCAGCACACAGCGATATGGTTA 8 114 0 AGCACCACGC 0.710345 -187 GTAGGGGTTTGGGTACGCGCAGGGACGTGGAGG 8 156 1 GGGTCCGCGG 0.912584 -145 TTTGTGTGTGGGGTACATGCGGTATGCCGCAGT 8 215 1 GGGTCTGCGT 0.511035 -86 GCCGCTGATACGCCGCAAGCTGTCTTCCACAAC 9 30 0 CGCCCAGCGT 0.942608 -246 TTCAGAGAACAGACGCGCGCGATCACACAACAC 9 71 0 AGACCCGCAT 0.855998 -205 CACAAGCGACGCACACTCACGGCCTATTCCTGC 9 118 0 GCACCCACGC 0.932548 -158 AAATACCCATGCACACAAGCGACGCACACTCAC 9 131 0 GCACCAGCAC 0.599175 -145 ATCCGTTTTTACCAGCGCGCTCTTTCCCCTCAT 9 185 1 ACCACCGCCT 0.667632 -91 CTCATCTTTTGCCTTCGTGCCGTTATTATCCGA 9 213 1 GCCTCTGCGT 0.813499 -63 TTATTATCCGAGTTGCTCGCAGTATGCCTATGA 9 235 1 AGTTCCGCGT 0.89933 -41 CCATGTACTCGCACGCTCTCATAGGCATA 9 257 0 ACTCCCGCCT 0.867897 -19 TCAGTCACCAGCACACACGCCGGAGAAACTATA 10 25 0 GCACCCGCGG 0.985806 -48 ACACACCTCTAGCCTCTCGCAAGACAGTTTCGC 11 39 0 AGCCCCGCAG 0.943883 -133 **** * *** ** Masking position 6 Map Score: 43.9777 Number of sites scoring better than the average of aligned sites = 2790 Number in coding regions = 2564 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 2 CCCAAGACGACCGCGCGTGGGTAGAAAGCTGC 1 35 1 CCGCGCTGGT 0.721369 -266 TCGGTTTCTCGCCCTCGGTGGTTACTCCTTGT 1 149 0 GCCCTCGGGT 0.936129 -152 CATGGCCCGCGCGCAGGTACGTTTGTCAGGTC 1 179 0 GCGCAGTCGT 0.973541 -122 ACCCCGCCACCCGCTGCATCCCTTGACACTTC 1 234 0 CCGCTGACCC 0.907163 -67 TTTTCACGGCGCAGTTACCTGCAAGGAGC 2 10 0 GCGCAGTCCT 0.966574 -20 TGCTCTGCAAGGTGCGTGAGCGA 3 2 1 GCTCTGAGGT 0.876969 -85 ATGCTCTGTGTCCTCCTCATGTGA 5 57 0 GCTCTGGCCT 0.940298 -14 TGCATCCCGTGCCCTGAAAGCTGCTCTAATCC 7 127 0 GCCCTGAGCT 0.915099 -174 ACGGCGCCACGCGCAGCGCCGCGGGCAGCGTG 7 194 0 GCGCAGGCGC 0.961071 -107 TGAGCTAATAGCCCACGGCGCCACGCGCAGCG 7 208 0 GCCCACGGCC 0.815164 -93 AAGTGTGCGCGGTGTGCTGATAGTACAT 8 7 1 GCGCGGGGCT 0.961201 -294 CGTAACCATATCGCTGTGTGCTGCTTTTAACC 8 112 1 TCGCTGGGCT 0.828453 -189 GTTTGGGTACGCGCAGGGACGTGGAGGGACTC 8 162 1 GCGCAGGCGT 0.982282 -139 CGCACAGCAGCCGCTGATACGCCGCAAGCTGT 9 40 0 CCGCTGTCGC 0.962585 -236 TCTGAATTTACCGCTGAAAGGCAGGAATAGGC 9 98 1 CCGCTGAGGC 0.923356 -178 ATTGTTGCTCGCGCTGATCCGTTTTTACCAGC 9 169 1 GCGCTGTCGT 0.989166 -107 TTTTACCAGCGCGCTCTTTCCCCTCATCTTTT 9 191 1 GCGCTCTCCC 0.958935 -85 GTACTCGCACGCTCTCATAGGCATACTGCGAG 9 250 0 GCTCTCTGGC 0.827327 -26 CTTGCCCTGCTGCGTATAGTTTCTC 10 4 1 GCCCTGTCGT 0.814693 -69 ****** * *** Masking position 4 Map Score: 28.8213 Number of sites scoring better than the average of aligned sites = 1515 Number in coding regions = 1418 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 CCTGCGCGCGGGCCATGGCGGAGTCTATTCTCG 1 194 1 GGCCTGGCGG 0.899924 -107 CCTTGACACTTCCATCAGCCGAGAATAGACTCC 1 213 0 TCCACAGCGG 0.981158 -88 CGTTGCCTTGACCAAAGGCTGAGAATGCGGGAA 1 274 1 ACCAAGGCGG 0.896739 -27 ACACGCGCTTGACTGCAGCTGAGAGGAGGGATT 3 46 1 GACTCAGCGG 0.953787 -41 CTACAGGGTAGGCAAAACCGGCGCGCCTAT 6 8 0 GGCAAACCGG 0.971679 -68 GGGGTCAGCGTACACAACCGGTGAAAAAAGAGG 6 42 1 TACAAACCGG 0.883979 -34 AGGTGCTAGTGCCTTCACCGGCGTGGGAGTTCA 7 15 0 GCCTCACCGG 0.925016 -286 GGGCACGGGATGCAAAGGCGGCGTACTTGACAA 7 145 1 TGCAAGGCGG 0.972376 -156 AATACACGCTGCCCGCGGCGCTGCGCGTGGCGC 7 190 1 GCCCCGGCCG 0.871015 -111 AGGGCGTTGCTCTACCAGCTGAGCTAATAGCCC 7 226 0 TCTACAGCGG 0.760184 -75 AACCCCTACCGACACAGCCCGGGTTAAAAGCAG 8 132 0 GACAAGCCGG 0.958914 -169 GCAGTTTTTTTACAGCAGCGGCGTTGCTCGTTT 8 243 1 TACACAGCGG 0.969667 -58 CTGAAAGGCAGGAATAGGCCGTGAGTGTGCGTC 9 111 1 GGAAAGGCGG 0.858168 -165 ACGGCACGAAGGCAAAAGATGAGGGGAAAGAGC 9 203 0 GGCAAAGAGG 0.838307 -73 GTCAGATGTTGACCGCAGCAGGGAAAAGGCGAT 11 139 1 GACCCAGCGG 0.978691 -33 **** **** * * Masking position 13 Map Score: 14.2265 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 607 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 GGGTATCGATTGGCGGACACGCCAGCC 1 4 0 TGCGCACGCA 0.840717 -297 CGCCAATCGATACCCAAGACGACCGCGCGTGGGT 1 23 1 TCCCGACGCC 0.957797 -278 CCTGCACTCCGTTCGCTCACGCACCTTGCAGAGC 3 12 0 GTCGCACGAC 0.727057 -75 CCCTCATCCCCATCACGCCACCTGCCGCTT 4 38 0 TCCCCACGCA 0.983232 -20 ATCTCTCTTTCTCTGTTCACAAACCATACAACTG 5 11 0 CCTGCACAAC 0.714178 -60 GTAGGGGGGTCAGCGTACACAACCGGTGAAAAAA 6 37 1 CGCGCACACC 0.915913 -39 AAAACTATATTTCCCACCATGGAAGGGTTTTCTT 7 83 0 TCCCCATGAA 0.822796 -218 GCACAAACTGCTCCCTGCATGTACTATCAGCACA 8 23 0 CCCCCATGAC 0.951162 -278 ACACGCTGCCTACCGTGCACAAACTGCTCCCTGC 8 39 0 TCCGCACAAC 0.978729 -262 TCTTCACCTGTGCCCGCCACGTACACTTACACGC 8 67 0 TCCCCACGAC 0.995337 -234 ACCCAAACCCCTACCGACACAGCCCGGGTTAAAA 8 136 0 CACCCACACC 0.938206 -165 ATGTTCATGAGTCCCTCCACGTCCCTGCGCGTAC 8 168 0 GCCCCACGCC 0.985142 -133 ATACCGCATGTACCCCACACACAAACGAGGTAAA 8 206 0 TCCCCACAAA 0.957788 -95 CGCGCGCGATCACACAACACGCACAGCAGCCGCT 9 57 0 CCACCACGAC 0.917033 -219 CGCGACTCAGTCACCAGCACACACGCCGGAGAAA 10 30 0 TACCCACAAC 0.929813 -43 GAGAACTCCCCGTAACAACCGCGACTCAGT 10 53 0 TCCCAACACC 0.881868 -20 * *** **** ** Masking position 9 Map Score: 16.4817 Number of sites scoring better than the average of aligned sites = 824 Number in coding regions = 737 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 GCGTGGGTAGAAAGCTGCGAGAGGGTCTGG 1 49 1 AAAGCTGCGA 0.603432 -252 TTACTCCTTGTATGCCGCGGGACTGGTCCT 1 130 0 TATGCCGCGG 0.959234 -171 AGTGTCAAGGGATGCAGCGGGTGGCGGGGT 1 236 1 GATGCAGCGG 0.825964 -65 ATCCCTCCTCTCAGCTGCAGTCAAGCGCGT 3 48 0 TCAGCTGCAG 0.893418 -39 AAATGTATCTTAAGCGGCAGGTGGCGTGAT 4 27 1 TAAGCGGCAG 0.946403 -31 CGCCACGCGCAGCGCCGCGGGCAGCGTGTA 7 192 0 AGCGCCGCGG 0.967324 -109 CGTGTAAGTGTACGTGGCGGGCACAGGTGA 8 68 1 TACGTGGCGG 0.717065 -233 GCCCGGGTTAAAAGCAGCACACAGCGATAT 8 119 0 AAAGCAGCAC 0.7414 -182 GTACATGCGGTATGCCGCAGTTTTTTTACA 8 227 1 TATGCCGCAG 0.943401 -74 CAGTTTTTTTACAGCAGCGGCGTTGCTCGT 8 244 1 ACAGCAGCGG 0.970537 -57 TTGGATGACCAGAGCAGCAGATAAAAACGA 8 270 0 AGAGCAGCAG 0.94671 -31 CAGCCGCTGATACGCCGCAAGCTGTCTTCC 9 35 0 TACGCCGCAA 0.820697 -241 CACAACACGCACAGCAGCCGCTGATACGCC 9 49 0 ACAGCAGCCG 0.845007 -227 GGAGAAACTATACGCAGCAGGGCAAG 10 7 0 TACGCAGCAG 0.973553 -66 TGCTGGTGACTGAGTCGCGGTTGTTACGGG 10 45 1 TGAGTCGCGG 0.767177 -28 TCAGATGTTGACCGCAGCAGGGAAAAGGCG 11 140 1 ACCGCAGCAG 0.959641 -32 ********** Masking position 4 Map Score: 16.4779 Number of sites scoring better than the average of aligned sites = 1147 Number in coding regions = 1069 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 CCGCGGGACTGGTCCTACTCCTCTACCGAGCGGT 1 112 0 GGTCTACTTT 0.942243 -189 GCCCTCGGTGGTTACTCCTTGTATGCCGCGGGAC 1 137 0 GTTCTCCTTT 0.942243 -164 ATGCTCTGTGTCCTCCTCATGTGACTCATTTT 5 49 0 TGTCTCCTTT 0.98279 -22 ATAGGCGCGCCGGTTTTGCCTACCCTG 6 4 1 GGCCGCCGTT 0.925609 -72 GCCCCGGCCCTCCTCTTTTTTCACCGGTT 6 57 0 GGCCTCCTTT 0.988056 -19 TTTGGTCCTCTTGGTTTCCGTTGTGGA 9 4 1 GGTCTCTTTT 0.970943 -272 CGCGCGCGTCTGTTCTCTGAATTTACCGCTGAAA 9 83 1 TGTCTCTGTT 0.8809 -193 GTGTGTGCTCCTTATATTTTTTAAGGG 11 4 1 TGTCTCCTTT 0.98279 -168 *** ***** * * Masking position 12 Map Score: 4.7639 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 81 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 GGCTGGCGTGTCCGCCAATCGATACC 1 7 1 CGTGTCCGCC 0.979739 -294 GACAAACGTACCTGCGCGCGGGCCATGGCG 1 184 1 CCTGCGCGCG 0.918924 -117 AAGCGCGTGTCCTGCACTCCGTTCGCTCAC 3 26 0 CCTGCACTCC 0.937868 -61 ATGCTCTGTGTCCTCCTCATGTGACT 5 55 0 TGTGTCCTCC 0.880685 -16 GTAGGCAAAACCGGCGCGCCTAT 6 4 0 CCGGCGCGCC 0.966777 -72 GCCCCGGCCCTCCTCTTTTTTCA 6 63 0 CCGGCCCTCC 0.978329 -13 CTGAAGCTAGCGTGTCTGCCAATTCCACCA 7 46 1 CGTGTCTGCC 0.945128 -255 TCCAATACACGCTGCCCGCGGCGCTGCGCG 7 187 1 GCTGCCCGCG 0.950201 -114 ACACTTACACGCTGCCTACCGTGCACAAAC 8 49 0 GCTGCCTACC 0.807802 -252 CCTCTTCACCTGTGCCCGCCACGTACACTT 8 73 0 TGTGCCCGCC 0.966714 -228 TGGGGTACATGCGGTATGCCGCAGTTTTTT 8 223 1 GCGGTATGCC 0.557543 -78 TACGCCGCAAGCTGTCTTCCACAACGGAAA 9 25 0 GCTGTCTTCC 0.905306 -251 ACGGCCTATTCCTGCCTTTCAGCGGTAAAT 9 103 0 CCTGCCTTTC 0.678953 -173 GTGTGTGCTCCTTATATTTTT 11 2 1 TGTGTGCTCC 0.718969 -170 ********** Masking position 4 Map Score: 16.2556 Number of sites scoring better than the average of aligned sites = 764 Number in coding regions = 665 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 8 CTCGGCTGATGGAAGTGTCAAGGGATGCAG 1 223 1 GGAAGTGTCA 0.939178 -78 CCTCGATGGTGGAATTGGCAGACACGCTAG 7 52 0 GGAATTGGCA 0.994439 -249 AGCGTGTATTGGAATTGGCATTTTGTCAAG 7 170 0 GGAATTGGCA 0.994439 -131 CTGAAAGGCAGGAATAGGCCGTGAGTGTGC 9 111 1 GGAATAGGCC 0.960083 -165 GATCCTTGACAGAATTCGCACACACCTCTA 11 61 0 AGAATTCGCA 0.906861 -111 ********** Masking position 4 Map Score: 1.83002 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 24 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 CACCCGCTGCATCCCTTGACACTTCCATCA 1 229 0 ATCCCTTGAC 0.991547 -72 CTTTTGGACGTTGCCTTGACCAAAGGCTGA 1 266 1 TTGCCTTGAC 0.94567 -35 AGCTGCTCTAATCCCTTGACTAGAAAAACT 7 111 0 ATCCCTTGAC 0.991547 -190 CCGCCTTTGCATCCCGTGCCCTGAAAGCTG 7 136 0 ATCCCGTGCC 0.975875 -165 ********** Masking position 7 Map Score: 1.76789 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ********** No masking Map Score: 1.38088e-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: 1.38088e-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 12 ********** No masking Map Score: 1.38088e-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