AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iarcA_hpyl_opreg_100.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0026_HP0027 198 HP0026: citrate synthase (gltA), HP0027: isocitrate dehydrogenase (icd) #2 HP0140 230 L-lactate permease (lctP) #3 HP0141 56 L-lactate permease (lctP) #4 HP0193 214 fumarate reductase, cytochrome b subunit (frdC) #5 HP0506 203 conserved hypothetical secreted protein Motif number 1 TATATAACCCTTAAAAATCTTTTTTTGAATGCGTGTTT 1 60 1 TTAAATTTTA 0.88768 -139 TGAATGCGTGTTTAAAAGTAGCGGTTGGAAATAACTTG 1 85 1 TTAAAAGTTG 0.657958 -114 ATGATTTCTTTTAAAAACATTGCGTTTTTTCAAGTTAT 1 115 0 TTAAATTTTT 0.985797 -84 AAAGAAATCATTTAATTTTTTGGCTTATAATTAGGAGT 1 142 1 TTAATTTTTT 0.97282 -57 TTGACTTCCTTAAGTTTTGATAGCATTC 1 181 0 TTACTTTTTT 0.829241 -18 TATATTGTGTTTGAAACTCTTAATTTGGAATTTAAGGA 2 18 0 TTAAATTTTG 0.969679 -213 TAAATGCTACTTAAAATTAGTTTTTTCTTTTAAGTAAG 2 168 1 TTAAAGTTTT 0.970033 -63 CCTTGAATAATTAAAAGTATTTTTTTATCTTACTTAAA 2 196 0 TTAAATTTTT 0.969461 -35 AAATCCCTTTTTAAAAATATTCTCTTAGTGCTAGTTCT 3 25 0 TTAAATTTTG 0.969594 -32 CTAATAGCGTTTAAAAAATGTAAATTTTAAACAATAGC 4 55 1 TTAAAGTTTT 0.972247 -160 AATAGCCCCTTTGAATTGAATTTTTTCTCAATTTAGGT 4 87 1 TTAATATTTT 0.889086 -128 CTACTACATTTGAAATAATTTTTCTTATAAACAAAACC 4 122 0 TGAATTTTTT 0.826301 -93 ACGATACAAGTTTAAAGCCTGGCCTTGTTTTTATAGCT 5 111 0 TTAAATGTTT 0.949126 -93 ATCGTTTTTCTTTAATGGCTTATGTTATACTAATAAAA 5 144 1 TTAATTTTTT 0.972797 -60 AATGCCTTCAATCAAATCTGTATTTTATTAGTATAACA 5 166 0 ATAAAGTTTT 0.756758 -38 ** *** ** ** * Masking position 4 Map Score: 19.5787 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 372 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 TACTCAAACTTTAGAAAAAGGATAAACA 1 6 0 TTAGAAAAAT 0.937644 -193 GCAATGTTTTTAAAAGAAATCATTTAATTTTTT 1 130 1 TAAAAAAAAT 0.957018 -69 CTCCTAATTATAAGCCAAAAAATTAAATGATTT 1 146 0 TAAGCAAAAT 0.919438 -53 ACATTGTTACTAAAATAAACCACAAACCCATTA 2 120 1 TAAAAAAAAC 0.960196 -111 TTATCTTACTTAAAAGAAAAAACTAATTTTAAG 2 177 0 TAAAAAAAAC 0.960196 -54 TTCTTTTAAGTAAGATAAAAAAATACTTTTAAT 2 192 1 TAAGAAAAAA 0.926371 -39 CAAAACCTAAATTGAGAAAAAATTCAATTCAAA 4 96 0 ATTGAAAAAT 0.597764 -119 GTTTTGTTTATAAGAAAAATTATTTCAAATGTA 4 123 1 TAAGAAAAAT 0.983767 -92 CGGATTGATTAAAAAGAAAATACCCAACGCTAT 5 19 1 AAAAAAAAAC 0.905736 -185 TAAAACCATTTATGAGAAACCACCATGCATCAA 5 61 1 TATGAAAAAC 0.942167 -143 ATAAGCCATTAAAGAAAAACGATACAAGTTTAA 5 134 0 AAAGAAAAAT 0.960222 -70 ***** *** ** Masking position 7 Map Score: 11.3432 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 314 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 CCTTTTTCTAAAGTTTGAGTAACTATACTAGCGCA 1 18 1 AATGATACTA 0.688221 -181 TTCTTTTAAAAACATTGCGTTTTTTCAAGTTATTT 1 113 0 AATGCTTTTT 0.940989 -86 TATAAGCCAAAAAATTAAATGATTTCTTTTAAAAA 1 136 0 AATAATATTT 0.621332 -63 AGAAGGCTCCTTAAATTCCAAATTAAG 2 3 1 AATCCTAATT 0.938273 -228 CAAACCCATTAAATTTGACTTAATATTAAATGCTA 2 142 1 AATGATAATA 0.857888 -89 AAATTTTCCTTGAATAATTAAAAGTA 2 215 0 AATCCTAATA 0.946263 -16 TAAAAAATCCCTTTTTAAAAATATTCT 3 40 0 AATCCTTTTA 0.939354 -17 TGAACGATCCTTATTTTATAGGTGGTA 4 3 1 AATCCTTTTT 0.930417 -212 TATAGGTGGTAACTATCCCTTATTATATCTAATAG 4 27 1 AATCCTATTA 0.960383 -188 CTATTGTTTAAAATTTACATTTTTTAAACGCTATT 4 57 0 AATACTTTTT 0.78483 -158 TTGACGCAAAAACACTGCCTTAATTCTACTACATT 4 150 0 AATGCTAATT 0.947717 -65 ATTTTAGGTTAATTTTGAGTTTTTAGGAGCAGTTT 4 188 1 AATGATTTTA 0.841531 -27 TATGAGAAACCACCATGCATCAATAAAACGCGCTT 5 71 1 CATGCTAATA 0.76812 -133 ** *** * **** Masking position 2 Map Score: 9.48522 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 304 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 AAGTTTGAGTAACTATACTAGCGCAAAAAT 1 28 1 AACTATACTA 0.728652 -171 GTTATTTCCAACCGCTACTTTTAAACACGC 1 90 0 ACCGCTACTT 0.940282 -109 TTAGGAGTTGAATGCTATCAAAACTTAAGG 1 172 1 AATGCTATCA 0.738032 -27 AGAAGGCTCCTTAAATTCCAAA 2 3 1 AAGGCTCCTT 0.808761 -228 CTTAATATTAAATGCTACTTAAAATTAGTT 2 160 1 AATGCTACTT 0.950872 -71 TGAACGATCCTTATTTTATAGG 4 3 1 AACGATCCTT 0.828522 -212 ACATTTTTTAAACGCTATTAGATATAATAA 4 46 0 AACGCTATTA 0.965816 -169 ACACTGCCTTAATTCTACTACATTTGAAAT 4 144 0 AATTCTACTA 0.838555 -71 AAAAACTGCTCCTAAAAACTCAAA 4 201 0 ACTGCTCCTA 0.878687 -14 GAAAATACCCAACGCTATAAGACGAGATAA 5 34 1 AACGCTATAA 0.918396 -170 CGCGCTTCATAAAGCTATAAAAACAAGGCC 5 99 1 AAAGCTATAA 0.593463 -105 ATTAAAGAAAAACGATACAAGTTTAAAGCC 5 130 0 AACGATACAA 0.88509 -74 ********** Masking position 1 Map Score: 6.71555 Number of sites scoring better than the average of aligned sites = 1168 Number in coding regions = 1058 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 ATACTAGCGCAAAAATACTATATAACCCTTA 1 42 1 AAAAATCTAT 0.911391 -157 CGCTACTTTTAAACACGCATTCAAAAAAAGA 1 77 0 AAACACCATT 0.886323 -122 AATAACTTGAAAAAACGCAATGTTTTTAAAA 1 114 1 AAAAACCAAT 0.977196 -85 TTATAAGCCAAAAAATTAAATGATTTCTTTT 1 141 0 AAAAATAAAT 0.892495 -58 TAAGAGTTTCAAACACAATATAATACTCAAA 2 34 1 AAACACATAT 0.810078 -197 AAAATAAACCACAAACCCATTAAATTTGACT 2 131 1 ACAAACCATT 0.7976 -100 ACTTAAAAGAAAAAACTAATTTTAAGTAGCA 2 172 0 AAAAACAATT 0.940762 -59 AGTAAGATAAAAAAATACTTTTAATTATTCA 2 200 1 AAAAATCTTT 0.87453 -31 TAAAAAATCCCTTTTTAAAAATAT 3 43 0 AAAATCCTTT 0.659548 -14 TAAATTGAGAAAAAATTCAATTCAAAGGGGC 4 91 0 AAAAATCAAT 0.938179 -124 TCTTATAAACAAAACCTAAATTGAGAAAAAA 4 107 0 AAAACCAAAT 0.773737 -108 TGTTTATAAGAAAAATTATTTCAAATGTAGT 4 127 1 AAAAATATTT 0.792081 -88 AACTGCTCCTAAAAACTCAAAATTAACCTAA 4 191 0 AAAAACCAAA 0.808344 -24 CGGATTGATTAAAAAGAAAATACCCAACGCT 5 19 1 AAAAAGAAAT 0.752201 -185 GCCATTAAAGAAAAACGATACAAGTTTAAAG 5 132 0 AAAAACATAC 0.698588 -72 ****** **** Masking position 3 Map Score: 13.5785 Number of sites scoring better than the average of aligned sites = 1626 Number in coding regions = 1365 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 6 ACTTTTAAACACGCATTCAAAAAAAGATTTT 1 73 0 ACGCATTAAA 0.868632 -126 TAGGAGTTGAATGCTATCAAAACTTAAGGAA 1 173 1 ATGCTATAAA 0.956887 -26 CATTTTTTAAACGCTATTAGATATAATAAGG 4 44 0 ACGCTATAGA 0.986506 -171 AAAATACCCAACGCTATAAGACGAGATAAAA 5 35 1 ACGCTATAGA 0.986506 -169 GCGCTTCATAAAGCTATAAAAACAAGGCCAG 5 100 1 AAGCTATAAA 0.975086 -104 AGTATAACATAAGCCATTAAAGAAAAACGAT 5 144 0 AAGCCATAAA 0.946325 -60 ******* *** Masking position 7 Map Score: 4.23424 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 132 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 TCAAACTTTAGAAAAAGGATAAACA 1 6 0 GAAAAAGGAT 0.944753 -193 ACACGCATTCAAAAAAAGATTTTTAAGGGT 1 66 0 AAAAAAAGAT 0.940487 -133 GAATATTTTTAAAAAGGGATTTTTTA 3 41 1 AAAAAGGGAT 0.980577 -16 ACCACCTATAAAATAAGGATCGTTCA 4 7 0 AAATAAGGAT 0.961636 -208 TATTAGATATAATAAGGGATAGTTACCACC 4 31 0 AATAAGGGAT 0.925679 -184 TATACTAATAAAATACAGATTTGATTGAAG 5 169 1 AAATACAGAT 0.832445 -35 ********** Masking position 5 Map Score: 3.23871 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 144 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 AGTATAGTTACTCAAACTTTAGAAAAAGGAT 1 16 0 CTCAAACTTA 0.78807 -183 CTATATAACCCTTAAAAATCTTTTTTTGAAT 1 59 1 CTTAAAAATT 0.727532 -140 AATTTTTTGGCTTATAATTAGGAGTTGAATG 1 155 1 CTTATAATTG 0.952039 -44 GTGTTTGAAACTCTTAATTTGGAATTTAAGG 2 19 0 CTCTTAATTG 0.943463 -212 CAATATAATACTCAAAATTGGTAAGAAATTG 2 49 1 CTCAAAATTG 0.984143 -182 AACCCACTCGCTCAAACATTGTTACTAAAAT 2 105 1 CTCAAACATG 0.895485 -126 ACCACAAACCCATTAAATTTGACTTAATATT 2 138 1 CATTAAATTG 0.69966 -93 TTAAATGCTACTTAAAATTAGTTTTTTCTTT 2 167 1 CTTAAAATTG 0.974842 -64 TAAAAAAATACTTTTAATTATTCAAGGAAAA 2 207 1 CTTTTAATTT 0.643272 -24 CTCCTAAAAACTCAAAATTAACCTAAAATCG 4 186 0 CTCAAAATTA 0.914745 -29 ATGGTGGTTTCTCATAAATGGTTTTATCTCG 5 56 0 CTCATAAATG 0.927644 -148 CAAGGCCAGGCTTTAAACTTGTATCGTTTTT 5 122 1 CTTTAAACTG 0.824535 -82 ********* * Masking position 6 Map Score: 11.8217 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 312 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 9 TCCTTAAGTTTTGATAGCATTCAACTCCTA 1 173 0 TTGATAGCAT 0.804245 -26 ATACTCAAAATTGGTAAGAAATTGGTAAGA 2 56 1 TTGGTAAGAA 0.942994 -175 TGGTAAGAAATTGGTAAGATTGTAACCACA 2 67 1 TTGGTAAGAT 0.969933 -164 GTGGTTTATTTTAGTAACAATGTTTGAGCG 2 113 0 TTAGTAACAA 0.914493 -118 AAACTAATTTTAAGTAGCATTTAATATTAA 2 161 0 TAAGTAGCAT 0.901535 -70 TTTTTTCTTTTAAGTAAGATAAAAAAATAC 2 188 1 TAAGTAAGAT 0.916976 -43 ********** Masking position 5 Map Score: 0.404889 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 37 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ********** No masking Map Score: 6.2771e-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 11 ********** No masking Map Score: 6.2771e-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 12 ********** No masking Map Score: 6.2771e-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