AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i251_bsub_mtub_300.orf -o251_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 flgB 300 flagellar basal-body rod protein #2 fliF 45 flagellar basal-body M-ring protein #3 fliH 117 flagellar assembly protein #4 fliK 160 fliK #5 flgE 21 flagellar hook protein #6 fliL 251 flagellar protein #7 fliM 33 flagellar motor switch protein #8 cheY 25 two-component response regulator #9 flhA 32 flagella-associated protein #10 cheW 21 cheW #11 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #12 ndk 115 nucleoside diphosphate kinase #13 gerCA 162 heptaprenyl diphosphate synthase component I #14 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #15 mtrA 187 GTP cyclohydrolase I #16 hbs 300 non-specific DNA-binding protein HBsu Motif number 1 TTTTGAAGAAAAATGCAAAATTTATTAAAA 1 29 0 AAATGCAAAA 0.622777 -272 ATGCCGAAAAGAAAGGAGAAAAAACAGAAA 1 69 1 GAAAGGAGAA 0.758367 -232 TAAGCCTGAAAATAGCAGAATTTCTGTTTT 1 89 0 AATAGCAGAA 0.623598 -212 ATTTCTCCACAAAAGGAAAAAAGAAAACTT 3 33 1 AAAAGGAAAA 0.93327 -85 TTCAGCCTGCAAAAGGTGAGAATGATCAAT 3 81 0 AAAAGGTGAG 0.959415 -37 AACTTTCAGAACAAGGAAAGGGAACTCCTA 4 117 1 ACAAGGAAAG 0.866462 -44 CTGCTAAAAGCTGATCTTCAGAATT 4 146 0 AAAAGCTGAT 0.856434 -15 TTACTCTGTCAAATGGTAAGAAGTTTGTAG 6 138 1 AAATGGTAAG 0.640648 -114 AGTTTGTAGTAAAAGAAGATGAAGAAGCTG 6 159 1 AAAAGAAGAT 0.746478 -93 CGAAACACAAGGAGAGAGATAGATT 8 7 1 ACAAGGAGAG 0.928477 -19 TTTTCGATTTAAAAGGAGAGAAAAAACAGC 9 13 1 AAAAGGAGAG 0.983404 -20 GATCGTTGGGAAAGGCAGAGGTCTGATGCA 11 116 0 AAAGGCAGAG 0.854635 -121 AAATCAGCTGAAAAGCTGATTTTTTTATTG 11 148 1 AAAAGCTGAT 0.856434 -89 CCCCGCTGTTAAAAGCAAATGCTCGCAAAC 13 20 1 AAAAGCAAAT 0.88199 -143 TAAGCGAATGAAAAGATAAAACTCATACAT 13 100 1 AAAAGATAAA 0.462245 -63 ATGCCCCGCTAAAAGCAAAGTGAATGCCCT 15 119 0 AAAAGCAAAG 0.958629 -69 GGATGAAAAAAGGAAAAAAAGGAATAT 16 8 1 AAAAGGAAAA 0.93327 -293 GTCTCAGAAAAAAATGAGAGCAAGTAAGAG 16 203 0 AAAATGAGAG 0.734584 -98 ********** Masking position 9 Map Score: 16.1554 Number of sites scoring better than the average of aligned sites = 2198 Number in coding regions = 1780 Number in noncoding regions = 418 Number of orfs with sites within 600 bp upstream = 430 Fraction of orfs with sites within 600 bp upstream = 0.0690652 Motif number 2 TTTGAAACTTTTTGAAGAAAAATGCAAAAT 1 38 0 TTTGAAGAAA 0.852253 -263 AATAGATAATTGTGAGGACATTTTTTTACA 1 173 1 TGTGAGGACA 0.950225 -128 GGATATTGAGGGTGAAAAAAACTGAAATGG 1 269 1 GGTGAAAAAA 0.763448 -32 TTTTTCCTTTTGTGGAGAAATAGATGATTC 3 24 0 TGTGGAGAAA 0.979629 -94 AGAATACGGAGGTGAGGAAA 7 24 1 GGTGAGGAAA 0.973686 -10 ATCAATCCGGGGCGGAGAAATTTCTTAATA 12 21 0 GGCGGAGAAA 0.947529 -95 ATAATGATGGGGTGGAGAAT 12 106 1 GGTGGAGAAT 0.9211 -10 TGCTTTTAACAGCGGGGACAGCCAGC 13 7 0 AGCGGGGACA 0.737276 -156 TAAATGTGAATTTGGGGACAAGGGTGATAT 13 141 1 TTTGGGGACA 0.754477 -22 GGGGCTTTTCTGTGAAGAAATAAAGTGTAT 15 45 0 TGTGAAGAAA 0.976479 -143 TGTCCAACAAAGTGAAGAATTTCTGTATGT 16 124 0 AGTGAAGAAT 0.773004 -177 CAGACTGAACTGTGAAGAAATGATAATAAA 16 244 1 TGTGAAGAAA 0.976479 -57 ********** Masking position 8 Map Score: 11.203 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 514 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 CAGAAATTCTGCTATTTTCAGGCTTATATCA 1 93 1 GCTATTTCAG 0.883683 -208 CTATTTTCAGGCTTATATCAGGGCGAGAAAT 1 104 1 GCTTATACAG 0.968548 -197 TACTTTTCATGTTTTTAGCGGCAGAACCCGT 4 40 0 GTTTTTACGG 0.941208 -121 CTGAAGATCAGCTTTTAGCAG 4 150 1 GCTTTTACAG 0.992052 -11 GCGAGCATTTGCTTTTAACAGCGGGGACAGC 13 15 0 GCTTTTACAG 0.992051 -148 CATTCACTTTGCTTTTAGCGGGGCATATGTG 15 123 1 GCTTTTACGG 0.990429 -65 ******* *** Masking position 6 Map Score: 5.9644 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 62 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 GACGATTTAGAGAAAGAGTGGAATGACCGGGGGTTAAC 2 18 1 AAAGAATAGG 0.941446 -28 TTTTATGATTAAAGTAACCCGTTTGAACGGGCAGCCCTTT 6 46 1 AATAATTAGG 0.896161 -206 ACCATTTGACAGAGTAATTGTAGTATCCGGAAAACATTCA 6 115 0 AATAAATTGG 0.973952 -137 GTAAAGGTTTACATTAAAGTGAATAAAGGGTTGAATGGCA 11 73 1 AATAAATAGG 0.982025 -164 ATAGATTAAGAAATAAATGTGAATTTGGGGACAAGGGTGA 13 128 1 AAAAAATTGG 0.962315 -35 CGCTAAAAGCAAAGTGAATGCCCTGTCAGGAAGCCCATGC 15 103 0 AATGACTTGG 0.78977 -85 GCTAGAATCGAAATTAAATGTATTCATTGGTGGAGGACAT 15 153 1 AATAAATAGG 0.980932 -35 CGGCTTTTTAAGAAAAACTGCACTCTGAGGAATGTTTGTC 16 150 0 AAAAAATTGG 0.962308 -151 AGAGCAAGTAAGAGAAAGACAATTAAACGGCTTTTTAAGA 16 177 0 AAAAAATAGG 0.973954 -124 TGAAGAAATGATAATAAACGAACTGAATGTATCCTTTTGG 16 256 1 AATAAATAGT 0.826978 -45 * * *** * * * ** Masking position 7 Map Score: 5.89356 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 66 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 TTCTGCTATTTTCAGGCTTATATCAGGGCG 1 99 1 TTCAGGCTTA 0.795864 -202 TCTCACCTTTTGCAGGCTGAAGAGAACCCG 3 90 1 TGCAGGCTGA 0.907901 -28 AAAGCTGATCTTCAGAATTAGGAGTTCCCT 4 135 0 TTCAGAATTA 0.575503 -26 CGGGCAGCCCTTTACACTGAATGCGCTATT 6 73 1 TTTACACTGA 0.789831 -179 GTTGCTTATTTTCACAATGA 11 1 0 TTCACAATGA 0.903771 -236 AGAGGTCTGATGCACACTGCCATTCAACCC 11 100 0 TGCACACTGC 0.949264 -137 TGTATAGGCTTTCACACTGCACACCGAAAT 12 73 0 TTCACACTGC 0.967609 -43 TGTCCCCAAATTCACATTTATTTCTTAATC 13 131 0 TTCACATTTA 0.699376 -32 TGACAGGGCATTCACTTTGCTTTTAGCGGG 15 115 1 TTCACTTTGC 0.755241 -73 TAAGAAAAACTGCACTCTGAGGAATGTTTG 16 152 0 TGCACTCTGA 0.940012 -149 TTCTTCACAGTTCAGTCTGATTCTAAACCT 16 233 0 TTCAGTCTGA 0.935815 -68 ********** Masking position 4 Map Score: 5.55335 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 566 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 CCTTTCTTTTCGGCATTTTTGAAACTTTTT 1 55 0 CGGCATTTTT 0.855185 -246 ACCTCCATTTCAGTTTTTTTCACCCTCAAT 1 273 0 CAGTTTTTTT 0.789673 -28 GAAAAGATCGCAGCTTTCTACCGAAAAATA 6 194 1 CAGCTTTCTA 0.84588 -58 ATAAAAAAATCAGCTTTTCAGCTGATTTTA 11 146 0 CAGCTTTTCA 0.967993 -91 CCTTAGAAAGGGGCTTTTCTGTGAAGAAAT 15 54 0 GGGCTTTTCT 0.944638 -134 CCTTTCTAAGGGGCTTTTCATATTTCAAGA 15 73 1 GGGCTTTTCA 0.954591 -115 ATGCTTGATATGGCTTTTTATATGTGTTAC 16 91 1 TGGCTTTTTA 0.856865 -210 CCTCAGAGTGCAGTTTTTCTTAAAAAGCCG 16 160 1 CAGTTTTTCT 0.828582 -141 GACAATTAAACGGCTTTTTAAGAAAAACTG 16 170 0 CGGCTTTTTA 0.978792 -131 ********** Masking position 6 Map Score: 4.12831 Number of sites scoring better than the average of aligned sites = 1394 Number in coding regions = 1179 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 7 AATATATTCCCCCAGATGTTT 5 2 0 CCCAGATGTT 0.929587 -20 GTAATCGCTTCTCCGCTGTTTTATGATTAA 6 28 1 CTCCGCTGTT 0.985451 -224 AAATCAGCTTTTCAGCTGATTTTAGATCGT 11 140 0 TTCAGCTGAT 0.780689 -97 GCTGGCTGTCCCCGCTGTTAAAAGCAAAT 13 10 1 CCCCGCTGTT 0.993543 -153 GGCTGTATCCTCCCGCTGTTTGCGAGCATT 13 37 0 TCCCGCTGTT 0.985641 -126 ********** Masking position 7 Map Score: 2.64557 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 237 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 TCGTCGGTCTCGACGAAAGGTCCGGCTAAT 4 11 0 CGACGAAAGG 0.948213 -150 TCGTCGAGACCGACGACGGGTTCTGCCGCT 4 25 1 CGACGACGGG 0.954753 -136 ACTTTCAGAACAAGGAAAGGGAACTCCTAA 4 118 1 CAAGGAAAGG 0.852489 -43 GGAGGGAGGGGAGGCGAGTA 6 1 1 GGAGGGAGGG 0.961597 -251 GACAGAATACGGAGGTGAGGAAA 7 21 1 GGAGGTGAGG 0.888576 -13 CCATTCGAGGAGGTGTCTCAC 10 6 1 CGAGGAGGTG 0.973382 -16 AAATCCTTGACGAGCAAGGGATTGACGCTT 16 57 1 CGAGCAAGGG 0.956356 -244 TATCCTTTTGGGAGGAGGTGAAAGGC 16 285 1 GGAGGAGGTG 0.957405 -16 ********** Masking position 3 Map Score: 2.79991 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 208 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 CAAAAATGCCGAAAAGAAAGGAGAAAAAAC 1 64 1 GAAAAGAAAG 0.902103 -237 AAAGAAAGGAGAAAAAACAGAAATTCTGCT 1 76 1 GAAAAAACAG 0.977041 -225 GAAGTTCGTGTAAAAAAATGTCCTCACAAT 1 181 0 TAAAAAAATG 0.81561 -120 CTTATTGTAAGAAATAACAGGCATAAAGTC 1 214 0 GAAATAACAG 0.905078 -87 ATTGAGGGTGAAAAAAACTGAAATGGAGGT 1 273 1 AAAAAAACTG 0.831673 -28 TAAAAGGAGAGAAAAAACAGC 9 22 1 GAAAAAACAG 0.977041 -11 TGTAAACCTTTACAAAACAGAACAAAAACC 11 56 0 TACAAAACAG 0.673345 -181 ATACTAGGACAAAAAGACAGCGAGACTGGG 11 208 1 AAAAAGACAG 0.743869 -29 CATTATAGCATAAAAAAAAGAATTGGCTGT 13 61 0 TAAAAAAAAG 0.882383 -102 CATAGATTAAGAAATAAATGTGAATTTGGG 13 127 1 GAAATAAATG 0.77839 -36 ATGAAAAAAGGAAAAAAAGGAATATTCGTT 16 13 1 GAAAAAAAGG 0.875963 -288 ACCTGTCTCAGAAAAAAATGAGAGCAAGTA 16 207 0 GAAAAAAATG 0.940036 -94 ********** Masking position 4 Map Score: 12.2938 Number of sites scoring better than the average of aligned sites = 1173 Number in coding regions = 969 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 10 ********** No masking Map Score: 5.07571e-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: 5.07571e-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: 5.07571e-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