AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i314_bsub_mtub_300.orf -o314_bsub_mtub_300.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 trpE 215 anthranilate synthase #2 aroB 61 3-dehydroquinate synthase #3 aroF 69 chorismate synthase #4 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #5 ndk 115 nucleoside diphosphate kinase #6 gerCA 162 heptaprenyl diphosphate synthase component I #7 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #8 mtrA 187 GTP cyclohydrolase I #9 hbs 300 non-specific DNA-binding protein HBsu #10 PPE 300 PPE #11 cobD 113 cobD #12 hisC2 300 hisC2 Motif number 1 TTATATGTTGCCGGCTCTGTTGCTTATTTTC 4 18 0 CCGGCTCGTT 0.882044 -219 AGAACAAAAACCGGCGGCGTTATATGTTGCC 4 37 0 CCGGCGGGTT 0.981758 -200 AGAAATTTCTCCGCCCCGGATTGATTAATTA 5 26 1 CCGCCCCGAT 0.955342 -90 TTGGCTGTATCCTCCCGCTGTTTGCGAGCAT 6 38 0 CCTCCCGTGT 0.555257 -125 CGGTGAGAATCCGGCGCGGTCCCGCCACTGT 10 44 1 CCGGCGCGTC 0.992787 -257 CGGCGCGGTCCCGCCACTGTCACCGGGGAGC 10 55 1 CCGCCACGTC 0.989987 -246 TCGTAAGCCACGGCCACAGGCTGGAAGGCGA 10 91 1 CGGCCACGGC 0.97447 -210 TCGGGGTACACCGCCCCGGGTGGCAGGACGC 10 161 0 CCGCCCCGGT 0.98491 -140 GACGACACCTCCGCCGGCGGTCAGCCGCCG 10 281 1 CCGCCGGGGT 0.9916 -20 TGCCGCCGGGTTCAACAGGTCGG 11 3 1 CCGCCGGTTC 0.98079 -111 CACGATGAAGCGGCCAGCTACCCGGGTTGCC 11 32 0 CGGCCAGTAC 0.719669 -82 TCCGGCAGCGTCGCACACGTGG 11 102 0 CCGGCAGGTC 0.974741 -12 CGAATCTCTTCGGGCGCGCTCTTTACTAGCG 12 29 0 CGGGCGCCTC 0.82299 -272 CGTTGAGCTACGGGCGCTTGTCTTCAGTTGT 12 98 1 CGGGCGCTGT 0.895449 -203 AATCCTCTCGCCTCCGCAGTCCTTTAGGGGA 12 130 0 CCTCCGCGTC 0.95866 -171 ACTCCCCGAGCCGCCGGAGGCCTAGCGTACA 12 257 1 CCGCCGGGGC 0.995334 -44 GCGTACACAGCCGCCACATATGCTGTCGAC 12 281 1 CCGCCACTAT 0.863902 -20 ******* *** Masking position 5 Map Score: 27.3983 Number of sites scoring better than the average of aligned sites = 1564 Number in coding regions = 1409 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 2 TTGAGTTAGAGAATAGGGTAGCAGAGAATGAGTTTAG 1 67 1 GTGGAGAGAA 0.675045 -149 AGGAGAATGAGAAGATGGCATGAGAGGATAAAATACT 1 169 0 GGGGATAGAG 0.850631 -47 GCGTTAATGCGATGAAGGGAGAAGAAGTC 3 51 1 GGGGAGAGAG 0.987557 -19 AGTGAATGCCCTGTCAGGAAGCCCATGCTCTTGAAAT 8 94 0 CTGGAGCCAG 0.983285 -94 CTGAATGTATCCTTTTGGGAGGAGGTGAAAGGC 9 278 1 CTGGAGAGGG 0.974035 -23 AGGCGATGACGATGCAGGAAGCCGGTGAGAATCCGGC 10 22 1 GGGGAGCGGG 0.996389 -279 GCCACGGCCACAGGCTGGAAGGCGAGGCAAGCAACGA 10 97 1 CGGGAGCGAG 0.994218 -204 GTACACCGCCCCGGGTGGCAGGACGCGATGACGCGAG 10 150 0 CGGGAGACGG 0.987799 -151 CGGCGGCTGACCGCCGGCGGAGGTGTCGTCGC 10 279 0 GGCGCGCGGG 0.894902 -22 CCGGGTTCAACAGGTCGGCAACCCGGGTAGCTGGCCG 11 16 1 CGGGAACCGG 0.936203 -98 GTCATAAATAGCTGAGCGTAGACCACGTGTGCGACGC 11 80 1 GGCGAGCCAG 0.971119 -34 AGTCCGGGTACTCTCGGGAAGTCCATGGAGGCGTGCC 12 223 0 CTGGAGCCAG 0.983284 -78 GGCCTCCGGCGGCTCGGGGAGTCCGGGTACTCTCGGG 12 242 0 GTGGAGCCGG 0.989518 -59 * * ** ** *** * Masking position 8 Map Score: 17.8113 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 382 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 TTCTAATTGCTTTATACACACTCTTGTGTATTTCTAAGCTGTTCT 1 18 0 TTTAATTTCT 0.983327 -198 AAAGACTTCTTTTGGGTAGAATAAACATAATGTCTCAGCTCAACT 1 102 0 TTTAATGTCT 0.962063 -114 CCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGT 2 20 0 TTTAATTTCT 0.983327 -42 AATTGTATTGTTTCAATAAAAAAATCAGCTTTTCAGCTGATTTTA 4 146 0 TTTAATTTCA 0.892457 -91 TTTTTGTAGATATTAAGAAATTTCTCCGCCCCGGA 5 1 1 TTTAATTTCT 0.983327 -115 ATATCACCCTTGTCCCCAAATTCACATTTATTTCTTAATCTATGT 6 126 0 TGTAATTTCT 0.92481 -37 ATACACTTTATTTCTTCACAGAAAAGCCCCTTTCTAAGGGGCTTT 8 45 1 TTTAATTTCT 0.983327 -143 TGAGGAATGTTTGTCCAACAAAGTGAAGAATTTCTGTATGTAGAG 9 120 0 TTGAATTTCT 0.93234 -181 AGTGCAGTTTTTCTTAAAAAGCCGTTTAATTGTCTTTCTCTTACT 9 166 1 TTCAATGTCT 0.855596 -135 TTTATTATCATTTCTTCACAGTTCAGTCTGATTCTAAACCTGTCT 9 229 0 TTTAAATTCT 0.892457 -72 *** * * ***** Masking position 10 Map Score: 6.74285 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 76 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 TAAAATTCCCTCGACAGTTTTCTCATA 2 45 0 CCCTCGACAG 0.974868 -17 TATAATGATACCTGCGTAAGCGAATGAAAA 6 84 1 CCTGCGTAAG 0.941377 -79 ATGAAAAGCCCCTTAGAAAGGGGCTTTTCT 8 64 0 CCTTAGAAAG 0.930553 -124 CTCATTTTTTTCTGAGACAGGTTTAGAATC 9 215 1 TCTGAGACAG 0.790894 -86 GGGTCGCTCCCCGGTGACAGTGGCGGGACC 10 61 0 CCGGTGACAG 0.917415 -240 CGGGGAGCGACCCTCGTAAGCCACGGCCAC 10 78 1 CCCTCGTAAG 0.940883 -223 GGCGGTGTACCCCGAGAAAGCTAACCGGTC 10 177 1 CCCGAGAAAG 0.971078 -124 ACCTTCTGATCCGTAGTCAGATGCTCTATC 12 68 1 CCGTAGTCAG 0.934897 -233 ********** Masking position 9 Map Score: 4.29442 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 241 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 ATGTATGTATAGGCTTTCACACTGCACACCGAAAT 5 73 0 AGGCTTACGC 0.994323 -43 CTTCCTGACAGGGCATTCACTTTGCTTTTAGCGGG 8 110 1 GGGCTTACGC 0.99747 -78 TCTTCCCGTCAGGCGATGACGATGCAGGAAGCCGG 10 12 1 AGGCATACGC 0.991885 -289 TCTAGCGGTCGGGCCACCACCACGCTGCTGGGCCT 10 225 1 GGGCACACGC 0.992001 -76 CCACGCTGCTGGGCCTTAACGTGGCTGCTCGCGAC 10 244 1 GGGCTTACGC 0.99747 -57 **** ** ** ** Masking position 9 Map Score: 3.88903 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 11 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 ATTCTAATTGCTTTATACACACTCTTGTGT 1 34 0 CTTTATACAC 0.891617 -182 CCATTCAACCCTTTATTCACTTTAATGTAA 4 81 0 CTTTATTCAC 0.97089 -156 CATACACGATCTATATTCACAA 8 3 0 CTATATTCAC 0.89164 -185 CATACACTTTATTTCTTCACAGAAAAGCCC 8 44 1 ATTTCTTCAC 0.970891 -144 TACATACAGAAATTCTTCACTTTGTTGGAC 9 123 1 AATTCTTCAC 0.891641 -178 GTTTATTATCATTTCTTCACAGTTCAGTCT 9 245 0 ATTTCTTCAC 0.970891 -56 ********** Masking position 6 Map Score: 3.23333 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 88 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 GCTGGCTGTCCCCGCTGTTAAAAG 6 4 1 GGCTGTCCCG 0.963154 -159 GTCACCGGGGAGCGACCCTCGTAAGCCACGG 10 73 1 AGCGACCCCG 0.978068 -228 CCGGGAGCCAGGAGACTCGCGTCATCGCGTC 10 135 1 GGAGACTCCG 0.892729 -166 CATCGCGTCCTGCCACCCGGGGCGGTGTACC 10 157 1 TGCCACCCGG 0.89186 -144 GCCTTAACGTGGCTGCTCGCGACGCGACGAC 10 256 1 GGCTGCTCCG 0.989532 -45 TGAAGCGGCCAGCTACCCGGGTTGCCGACCT 11 27 0 AGCTACCCGG 0.968718 -87 CTCATACGGCAGCTATCCACGATGAAGCGGC 11 49 0 AGCTATCCCG 0.88775 -65 AGCCCCATTCGGCCGCTCTGGCACGCCTCCA 12 204 1 GGCCGCTCGG 0.977374 -97 CGGGGAGTCCGGGTACTCTCGGGAAGTCCAT 12 234 0 GGGTACTCCG 0.927104 -67 CTAGGCCTCCGGCGGCTCGGGGAGTCCGGGT 12 251 0 GGCGGCTCGG 0.984322 -50 ******** ** Masking position 8 Map Score: 9.45155 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 243 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TGCTCTCACTCCTTATGGCAAGG 1 203 0 TCTCACTCCT 0.651015 -13 GAGGTCTGATGCACACTGCCATTCAACCCT 4 99 0 GCACACTGCC 0.926632 -138 ACTCTCCCAGTCTCGCTGTCTTTTTGTCCT 4 213 0 TCTCGCTGTC 0.781711 -24 GCTGGCTGTCCCCGCTGTTA 6 1 1 GCTGGCTGTC 0.93218 -162 GGCTTACGAGGGTCGCTCCCCGGTGACAGT 10 70 0 GGTCGCTCCC 0.941565 -231 ACGCGAGTCTCCTGGCTCCCGGATCGTTGC 10 127 0 CCTGGCTCCC 0.968658 -174 CGGGCCACCACCACGCTGCTGGGCCTTAAC 10 234 1 CCACGCTGCT 0.923991 -67 TGGGCCTTAACGTGGCTGCTCGCGACGCGA 10 253 1 CGTGGCTGCT 0.880483 -48 CGGCGGCTGACCGCCGGCGGAGGTG 10 286 0 GCTGACCGCC 0.886276 -15 AACCCGGGTAGCTGGCCGCTTCATCGTGGA 11 35 1 GCTGGCCGCT 0.912215 -79 ACCACGTGTGCGACGCTGCCGGA 11 101 1 CGACGCTGCC 0.880079 -13 ATCTCTTCGGGCGCGCTCTTTACTAGCGCA 12 27 0 GCGCGCTCTT 0.650516 -274 GCCGAATGGGGCTCACTGCTAATGAGTTGT 12 187 0 GCTCACTGCT 0.943741 -114 CCGAGAGTACCCGGACTCCCCGAGCCGCCG 12 243 1 CCGGACTCCC 0.807717 -58 ********** Masking position 6 Map Score: 11.2313 Number of sites scoring better than the average of aligned sites = 2212 Number in coding regions = 2029 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 9 ATCAAATTGACCGCATTAGAGAAAAT 2 1 1 ATAATGGCAT 0.921776 -61 CCGCTGTTAAAAGCAAATGCTCGCAAACAGCGGGAG 6 22 1 AAAATGGCAA 0.977573 -141 AGCATAAAAAAAAGAATTGGCTGTATCCTCCCGCTG 6 49 0 AAAATGGTAT 0.96489 -114 TCTGTGAAGAAATAAAGTGTATGTAAGCTAGATGCA 8 31 0 AAAATGGTAA 0.954763 -157 CTAGAATCGAAATTAAATGTATTCATTGGTGGAGGA 8 154 1 AAAATGTCAT 0.880416 -34 CCTGTCTCAGAAAAAAATGAGAGCAAGTAAGAGAAA 9 200 0 AAAATGGCAA 0.977574 -101 AATGATAATAAACGAACTGAATGTATCCTTTTGGGA 9 262 1 AAAATGGTAT 0.96489 -39 ** ** ** **** Masking position 6 Map Score: 2.09802 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 58 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 TCTCTGCTACCCTATTCTCTAACTCAACTC 1 64 0 CCTATTCTCT 0.951214 -152 CTCAACTAAACTCATTCTCTGCTACCCTAT 1 79 0 CTCATTCTCT 0.966448 -137 ATGCCATCTTCTCATTCTCCTTGCCATAAG 1 185 1 CTCATTCTCC 0.965792 -31 ATATTCTCCACATTTTCTCTAATGCGGTCA 2 18 0 CATTTTCTCT 0.775582 -44 ACAGTTTTCTCATATTCTCCACATTTTCTC 2 29 0 CATATTCTCC 0.86591 -33 GACTTCTTCTCCCTTCATCGCA 3 58 0 CTTCTTCTCC 0.787567 -12 CTCTACTCTCCCAGTCTCGCTGTCTTTTT 4 218 0 CCCAGTCTCG 0.865076 -19 TGTCAGGAAGCCCATGCTCTTGAAATATGA 8 90 0 CCCATGCTCT 0.951562 -98 AAGCGTCAATCCCTTGCTCGTCAAGGATTT 9 57 0 CCCTTGCTCG 0.873967 -244 CCGTTTAATTGTCTTTCTCTTACTTGCTCT 9 187 1 GTCTTTCTCT 0.661767 -114 ********** Masking position 8 Map Score: 3.07106 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 390 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 11 CATTCTAATTGCTTTATACACACTCTTGTGT 1 34 0 GCTTTATACC 0.766183 -182 GCTGGCTGTCCCCGCTGTTAAAAGC 6 5 1 GCTGTCCCCC 0.917913 -158 AAAAGAATTGGCTGTATCCTCCCGCTGTTTG 6 45 0 GCTGTATCCC 0.970279 -118 GCCACCCGGGGCGGTGTACCCCGAGAAAGCT 10 168 1 GCGGTGTACC 0.986852 -133 ACCGCCGGCGGAGGTGTCGTCGCGTCGCGAG 10 271 0 GAGGTGTCGC 0.858617 -30 CGTCGCACACGTGGTCTACGCTCAGCTATTT 11 85 0 GTGGTCTACC 0.868928 -29 CTTGTCTTCAGTTGTGTCCCCTAAAGGACTG 12 114 1 GTTGTGTCCC 0.970256 -187 CACTGCTAATGAGTTGTCCCCCTTCAAGGGG 12 173 0 GAGTTGTCCC 0.891003 -128 ATATGTGGCGGCTGTGTACGCTAGGCCTCCG 12 271 0 GCTGTGTACC 0.983509 -30 ********* * Masking position 5 Map Score: 5.29278 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 250 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 CTTTTTGCTGAAAAATATGTTATA 3 3 1 TTTTCTGAAA 0.974463 -67 GTTATAGTAGTCTTACTTAAAAGCGTTAATGC 3 29 1 TCTTCTTAAA 0.883002 -41 AAGCTGATTTTTTTATTGAAACAATACAATTT 4 160 1 TTTTTTGAAC 0.78241 -77 AAACAATACAATTTCCTGATAAAACAAGCTAT 4 178 1 ATTTCTGAAA 0.895509 -59 AATCGTAACATCTTTCTGATAATTAATCAATC 5 44 0 TCTTCTGAAA 0.965291 -72 CAGAGTGCAGTTTTTCTTAAAAAGCCGTTTAA 9 163 1 TTTTCTTAAA 0.916736 -138 TGCTCTCATTTTTTTCTGAGACAGGTTTAGAA 9 211 1 TTTTCTGAAC 0.96529 -90 **** **** ** Masking position 9 Map Score: 1.5253 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 135 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 13 AGAAGATGGCATGAGAGGATAAAATACTATATAA 1 163 0 ATAAGAAAAA 0.972647 -53 AAACCTTTACAAAACAGAACAAAAACCGGCGGCG 4 49 0 AAAAGAAAAA 0.950146 -188 AAAACAAGCTATACTAGGACAAAAAGACAGCGAG 4 198 1 ATCAGAAAAA 0.928582 -39 CGCAGGTATCATTATAGCATAAAAAAAAGAATTG 6 66 0 ATAAGAAAAA 0.972646 -97 GCGTAAGCGAATGAAAAGATAAAACTCATACATA 6 97 1 ATAAAAAAAA 0.846179 -66 GGATGAAAAAAGGAAAAAAAGGAATATTC 9 6 1 AAAAGAAAAA 0.950146 -295 ** * ** * **** Masking position 6 Map Score: 0.432881 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 155 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 14 ********** No masking Map Score: -2.67631e-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 15 TACGATAAGAACAGCTTAGAAATAC 1 6 1 TAAGAACAGC 0.907639 -210 TCATTGTGAAAATAAGCAACAGAGCCG 4 8 1 GAAAATAAGC 0.910903 -229 CCCAACGATCTAAAATCAGCTGAAAAGCTG 4 136 1 TAAAATCAGC 0.895871 -101 GTTTCAATAAAAAAATCAGCTTTTCAGCTG 4 152 0 AAAAATCAGC 0.679746 -85 AATTTCCTGATAAAACAAGCTATACTAGGA 4 187 1 TAAAACAAGC 0.895534 -50 GCTCTTGAAATATGAAAAGCCCCTTAGAAA 8 75 0 TATGAAAAGC 0.716022 -113 ATGAAAAAAGGAAAAAAAGGAATATTCGTT 9 13 1 GAAAAAAAGG 0.679875 -288 GAGTAACACATATAAAAAGCCATATCAAGC 9 93 0 TATAAAAAGC 0.779798 -208 GGCTTTTTAAGAAAAACTGCACTCTGAGGA 9 159 0 GAAAAACTGC 0.71431 -142 GGACACAACTGAAGACAAGCGCCCGTAGCT 12 103 0 GAAGACAAGC 0.887109 -198 ********** Masking position 5 Map Score: 1.84859 Number of sites scoring better than the average of aligned sites = 1207 Number in coding regions = 1014 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261