AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i098_bsub_mtub_100.orf -o098_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 resD 80 two-component response regulator #2 resC 135 essential protein similar to cytochrome c biogenesis protein #3 phoP 211 two-component response regulator #4 yycF 300 similar to two-component response regulator [YycG] #5 senX3 173 senX3 #6 regX3 227 regX3 Motif number 1 GTGATGTCATGGCAGAGCTGAGCGGAAATTTTCTT 2 22 1 GGAGGTGGGG 0.973002 -114 CAATCTTCGGCGGGGCCATACGCGGGAATAAAGAT 2 91 1 CGGGCTAGGG 0.817439 -45 TTCTTTGAACCGGCCGCAGGGCCGGTTCTCCCT 4 9 0 CGCCCGGCGG 0.966419 -292 TTGATAAAGACGCACTCCGGTGAGGGGAGGTTTCA 4 54 1 CGACCGGGGG 0.992392 -247 CCGCCGAAACCGCCGGCAGGTGGGATCTCAAACAA 5 11 0 CGCGCGGGGA 0.959991 -163 CCGGCGGTTTCGGCGGCTGATGGTGTGCTTTGGTG 5 30 1 CGCGCGAGTG 0.942351 -144 GAACGGTAACCGAACAGCTGTGGCGTAGTGTGTGA 5 87 1 CGACGTGGCG 0.893287 -87 ATCCGGTGAACGTCGCCCTAGCGCGGCAAGGCCAA 5 133 0 CGCGCTACCG 0.667196 -41 CGCTCTGCATCGTCGTCGGCGCAGG 6 1 0 CGCGCGCCGG 0.970606 -227 CGATGCAGAGCGTAGCGATGAGGTGGGGGCACCAC 6 24 1 CGAGGTGGTG 0.990778 -204 CACTCTCCCCCGCAAGCGGGTGGTGCCCCCACCTC 6 43 0 CGAACGGGTG 0.984782 -185 CCGCTTGCGGGGGAGAGTGGCGCTGATGACCTGCG 6 59 1 GGAGGGGGTG 0.987932 -169 CGCTCTGCATCGTCGTCGGCGCAGGTCATCAGCGC 6 78 0 CGCGCGCCGG 0.970606 -150 CGATGCAGAGCGTAGCGATGAGGTGGGGGCACCAC 6 101 1 CGAGGTGGTG 0.990778 -127 CACTCTCCCCCGCAAGCGGGTGGTGCCCCCACCTC 6 120 0 CGAACGGGTG 0.984782 -108 CCGCTTGCGGGGGAGAGTGGCGCTGATGACCTGCG 6 136 1 GGAGGGGGTG 0.987932 -92 CGCTCTGCATCGTCGTCGGCGCAGGTCATCAGCGC 6 155 0 CGCGCGCCGG 0.970606 -73 CGATGCAGAGCGTAGCGATGAGGTGGGGGCACCAC 6 178 1 CGAGGTGGTG 0.990778 -50 CACTCTCCCCCGCAAGCGGGTGGTGCCCCCACCTC 6 197 0 CGAACGGGTG 0.984782 -31 CCGCTTGCGGGGGAGAGTGGCGCTG 6 213 1 GGAGGGGGTG 0.987932 -15 ** ** * ** * ** Masking position 2 Map Score: 46.0906 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 667 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 TATTTAATCGCTGTCCCAATCTTCGGCGGGG 2 75 1 CTGTCCCATC 0.95367 -61 GCTGTGCCTCCAGTATTATAAT 3 200 0 CTGTGCCCCA 0.909423 -12 CCTGCGCCGACGACGATGCAGA 6 2 1 CTGCGCCACG 0.996328 -226 CAAGCGGGTGGTGCCCCCACCTCATCGCTAC 6 35 0 GTGCCCCACC 0.99299 -193 CGCAGGTCATCAGCGCCACTCTCCCCCGCAA 6 63 0 CAGCGCCCTC 0.953016 -165 CGCTGATGACCTGCGCCGACGACGATGCAGA 6 79 1 CTGCGCCACG 0.996328 -149 CAAGCGGGTGGTGCCCCCACCTCATCGCTAC 6 112 0 GTGCCCCACC 0.99299 -116 CGCAGGTCATCAGCGCCACTCTCCCCCGCAA 6 140 0 CAGCGCCCTC 0.953016 -88 CGCTGATGACCTGCGCCGACGACGATGCAGA 6 156 1 CTGCGCCACG 0.996328 -72 CAAGCGGGTGGTGCCCCCACCTCATCGCTAC 6 189 0 GTGCCCCACC 0.99299 -39 CAGCGCCACTCTCCCCCGCAA 6 217 0 CAGCGCCCTC 0.953016 -11 ******* *** Masking position 6 Map Score: 28.2464 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 264 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 GTTTTCCCCCTGCTTTCCTTCTGTTA 1 65 0 CCCCCTGCTT 0.955643 -16 GTTTGAGATCCCACCTGCCGGCGGTTTCGGC 5 13 1 CCACCTGCCG 0.993329 -161 GGTGGTGCCCCCACCTCATCGCTACGCTCTG 6 29 0 CCACCTCATG 0.994283 -199 GGTGGGGGCACCACCCGCTTGCGGGGGAGAG 6 45 1 CCACCCGCTG 0.997764 -183 GGTGGTGCCCCCACCTCATCGCTACGCTCTG 6 106 0 CCACCTCATG 0.994283 -122 GGTGGGGGCACCACCCGCTTGCGGGGGAGAG 6 122 1 CCACCCGCTG 0.997764 -106 GGTGGTGCCCCCACCTCATCGCTACGCTCTG 6 183 0 CCACCTCATG 0.994283 -45 GGTGGGGGCACCACCCGCTTGCGGGGGAGAG 6 199 1 CCACCCGCTG 0.997764 -29 ********* * Masking position 5 Map Score: 22.2559 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 35 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 4 ATACGCGGGAATAAAGATAAAAAGGGCAGGC 2 108 1 ATAAGATAAA 0.965958 -28 TAAAAAGAGAGAAAGGCTTGCTTA 3 4 1 AAAAGAGAAA 0.96789 -208 CATTTATAGTAAAAAGAGAAAGGCTGTATTA 3 33 0 AAAAGAGAAA 0.96789 -179 TCTCTTTTTACTATAAATGAAAGCGCTATCA 3 45 1 CTAAAATGAA 0.631656 -167 ATCATTTTTAAAAGAAATAAAGACGTTTATG 3 74 0 AAAAAATAAA 0.881155 -138 AGATGACATAAAATAGAGAAATAGGATGTCG 3 165 1 AAAAGAGAAA 0.96789 -47 ACTTTTTTTAAAAAAGATAACTTTATTGAAA 4 84 0 AAAAGATAAC 0.900628 -217 ACCAGCATGACAATAGATAAACAACTGGCGA 4 117 1 CAAAGATAAA 0.96789 -184 ACAACTGGCGATAAAGGTGAAACATGTGTTT 4 137 1 ATAAGGTGAA 0.769949 -164 GGTTTAAGGTCAAAAGATAAAAAAAATAAAG 4 179 0 CAAAGATAAA 0.96789 -122 AACGAATGTTATATAGATGAAATGAAGTCAT 4 257 1 ATAAGATGAA 0.94673 -44 *** ******* Masking position 5 Map Score: 12.7943 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 499 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 5 ATTAAATACACAAGAAAGGCCGCATAAAGAA 2 52 0 CAAGAAGGCC 0.869075 -84 TCTTTATTCCCGCGTATGGCCCCGCCGAAGA 2 94 0 CGCGATGGCC 0.997056 -42 TTCGTTTCATCACTTATGGCCCATGTAAAGA 4 232 0 CACTATGGCC 0.987785 -69 TGCTTTGGTGCGCTGTTTGCCAAACAGCATG 5 55 1 CGCTTTTGCC 0.960946 -119 GTGACTTGTCCGATTTTGGCCTTGCCGCGCT 5 118 1 CGATTTGGCC 0.980548 -56 TTGGCCTTGCCGCGCTAGGGCGACGTTCACC 5 133 1 CGCGTAGGGC 0.92903 -41 GGGAGAGTGGCGCTGATGACCTGCGCCGACG 6 69 1 CGCTATGACC 0.987787 -159 GGGAGAGTGGCGCTGATGACCTGCGCCGACG 6 146 1 CGCTATGACC 0.987787 -82 **** ****** Masking position 1 Map Score: 10.7385 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 248 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 GATAAAAAGGGCAGGCCAAACCG 2 123 1 GCAGGCCAAA 0.417978 -13 TTTAGCGAAAGCAGGACATTCCGACAATTC 3 114 0 GCAGGACATT 0.563146 -98 GCTGTGCCTCCAGTATTATA 3 202 0 GCTGTGCCTC 0.827733 -10 CTATTGTCATGCTGGTCAACTTTTTTTAAA 4 103 0 GCTGGTCAAC 0.916911 -198 GCGCACCAAAGCACACCATCAGCCGCCGAA 5 38 0 GCACACCATC 0.898013 -136 TCATCGCTACGCTCTGCATCGTCGTCGGCG 6 15 0 GCTCTGCATC 0.972503 -213 GGTGGTGCCCCCACCTCATCGCTACGCTCT 6 30 0 CCACCTCATC 0.95084 -198 CGTCGTCGGCGCAGGTCATCAGCGCCACTC 6 73 0 GCAGGTCATC 0.988529 -155 TCATCGCTACGCTCTGCATCGTCGTCGGCG 6 92 0 GCTCTGCATC 0.972503 -136 GGTGGTGCCCCCACCTCATCGCTACGCTCT 6 107 0 CCACCTCATC 0.95084 -121 CGTCGTCGGCGCAGGTCATCAGCGCCACTC 6 150 0 GCAGGTCATC 0.988529 -78 TCATCGCTACGCTCTGCATCGTCGTCGGCG 6 169 0 GCTCTGCATC 0.972503 -59 GGTGGTGCCCCCACCTCATCGCTACGCTCT 6 184 0 CCACCTCATC 0.95084 -44 ********** Masking position 7 Map Score: 15.7099 Number of sites scoring better than the average of aligned sites = 1180 Number in coding regions = 1091 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 ACACAGTTCTCAAACTTTCTCACGATTTGA 1 24 1 CAAACTTTCT 0.903405 -57 TTTCTTTATGCGGCCTTTCTTGTGTATTTA 2 51 1 CGGCCTTTCT 0.972047 -85 TGTATTAAGCAAGCCTTTCTCTCTTTTTA 3 10 0 AAGCCTTTCT 0.983734 -202 TTGCTTAATACAGCCTTTCTCTTTTTACTA 3 28 1 CAGCCTTTCT 0.989596 -184 TTTTTTTTCTAAACCTTTATTTTTTTTATC 4 165 1 AAACCTTTAT 0.928556 -136 TTTTGACCTTAAACCGTTATAATAGACAAG 4 195 1 AAACCGTTAT 0.825941 -106 ********** Masking position 7 Map Score: 3.69369 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 263 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 8 TTCTGTTACTTTCATTTTATCAAATCGTGAG 1 42 0 TTCATTTATC 0.954639 -39 GCCTTTCTTGTGTATTTAATCGCTGTCCCAA 2 63 1 TGTATTTATC 0.954639 -73 AATAAAGACGTTTATGATAGCGCTTTCATTT 3 59 0 TTTATGAAGC 0.715544 -153 GTTTCATGATTTTATTTTAGCGAAAGCAGGA 3 128 0 TTTATTTAGC 0.927058 -84 ATTTCTCTATTTTATGTCATCTTAACATGTT 3 156 0 TTTATGTATC 0.954639 -56 GTGAAACATGTGTTTTTTTTCTAAACCTTTA 4 153 1 TGTTTTTTTC 0.608364 -148 TAAACCTTTATTTTTTTTATCTTTTGACCTT 4 174 1 TTTTTTTATC 0.939413 -127 CTATATAACATTCGTTTCATCACTTATGGCC 4 242 0 TTCGTTTATC 0.866233 -59 GCCGAATGACTTCATTTCATCTATATAACAT 4 262 0 TTCATTTATC 0.954639 -39 TTGTTTGAGATCCCACCTGCCG 5 2 1 TGTTTGAATC 0.686028 -172 ******* *** Masking position 5 Map Score: 4.9865 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 577 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 9 CCTTTGAAAGCGACACAGTTCTCAAACTTTC 1 12 1 CGACCAGTTC 0.621274 -69 AAGAAAATTTCCGCTCAGCTCTGCCATGACA 2 26 0 CCGCCAGCTC 0.96841 -110 AGGGAGAACCGGCCCTGCGGCCGGTTCAAA 4 10 1 CGGCCTGCGG 0.940777 -291 ATTGAAACCTCCCCTCACCGGAGTGCGTCTT 4 60 0 CCCCCACCGG 0.964968 -241 TCACACACTACGCCACAGCTGTTCGGTTACC 5 91 0 CGCCCAGCTG 0.982645 -83 CGGTGAACGTCGCCCTAGCGCGGCAAGGCCA 5 134 0 CGCCTAGCGC 0.962315 -40 AGCGGGTGGTGCCCCCACCTCATCGCTACGC 6 33 0 GCCCCACCTC 0.937162 -195 GGGGGCACCACCCGCTTGCGGGGGAGAGTGG 6 48 1 CCCGTTGCGG 0.667782 -180 AGGTCATCAGCGCCACTCTCCCCCGCAAGCG 6 60 0 CGCCCTCTCC 0.886205 -168 GCATCGTCGTCGGCGCAGGTCATCAGCGCCA 6 76 0 CGGCCAGGTC 0.876443 -152 AGCGGGTGGTGCCCCCACCTCATCGCTACGC 6 110 0 GCCCCACCTC 0.937162 -118 GGGGGCACCACCCGCTTGCGGGGGAGAGTGG 6 125 1 CCCGTTGCGG 0.667782 -103 AGGTCATCAGCGCCACTCTCCCCCGCAAGCG 6 137 0 CGCCCTCTCC 0.886205 -91 GCATCGTCGTCGGCGCAGGTCATCAGCGCCA 6 153 0 CGGCCAGGTC 0.876443 -75 AGCGGGTGGTGCCCCCACCTCATCGCTACGC 6 187 0 GCCCCACCTC 0.937162 -41 GGGGGCACCACCCGCTTGCGGGGGAGAGTGG 6 202 1 CCCGTTGCGG 0.667782 -26 CAGCGCCACTCTCCCCCGCAAGCG 6 214 0 CGCCCTCTCC 0.886205 -14 **** ****** Masking position 4 Map Score: 20.0537 Number of sites scoring better than the average of aligned sites = 2674 Number in coding regions = 2404 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 10 ********** No masking Map Score: 8.55083e-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: 8.55083e-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: 8.55083e-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