AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i251_chemotaxis_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 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 0.634092 -272 ATGCCGAAAAGAAAGGAGAAAAAACAGAAA 1 69 1 GAAAGGAGAA 0.767136 -232 TAAGCCTGAAAATAGCAGAATTTCTGTTTT 1 89 0 AATAGCAGAA 0.634903 -212 ATTTCTCCACAAAAGGAAAAAAGAAAACTT 3 33 1 AAAAGGAAAA 0.936225 -85 TTCAGCCTGCAAAAGGTGAGAATGATCAAT 3 81 0 AAAAGGTGAG 0.961261 -37 AACTTTCAGAACAAGGAAAGGGAACTCCTA 4 117 1 ACAAGGAAAG 0.87197 -44 CTGCTAAAAGCTGATCTTCAGAATT 4 146 0 AAAAGCTGAT 0.86229 -15 TTACTCTGTCAAATGGTAAGAAGTTTGTAG 6 138 1 AAATGGTAAG 0.651727 -114 AGTTTGTAGTAAAAGAAGATGAAGAAGCTG 6 159 1 AAAAGAAGAT 0.755539 -93 CGAAACACAAGGAGAGAGATAGATT 8 7 1 ACAAGGAGAG 0.931629 -19 TTTTCGATTTAAAAGGAGAGAAAAAACAGC 9 13 1 AAAAGGAGAG 0.984177 -20 GATCGTTGGGAAAGGCAGAGGTCTGATGCA 11 116 0 AAAGGCAGAG 0.860553 -121 AAATCAGCTGAAAAGCTGATTTTTTTATTG 11 148 1 AAAAGCTGAT 0.86229 -89 CCCCGCTGTTAAAAGCAAATGCTCGCAAAC 13 20 1 AAAAGCAAAT 0.886941 -143 TAAGCGAATGAAAAGATAAAACTCATACAT 13 100 1 AAAAGATAAA 0.474311 -63 ATGCCCCGCTAAAAGCAAAGTGAATGCCCT 15 119 0 AAAAGCAAAG 0.960509 -69 GGATGAAAAAAGGAAAAAAAGGAATAT 16 8 1 AAAAGGAAAA 0.936225 -293 GTCTCAGAAAAAAATGAGAGCAAGTAAGAG 16 203 0 AAAATGAGAG 0.743925 -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 ATTTTGCATTTTTCTTCAAAAAGTTTCAAA 1 38 1 TTTCTTCAAA 0.80797 -263 TGTAAAAAAATGTCCTCACAATTATCTATT 1 173 0 TGTCCTCACA 0.791691 -128 CCATTTCAGTTTTTTTCACCCTCAATATCC 1 269 0 TTTTTTCACC 0.901996 -32 GAATCATCTATTTCTCCACAAAAGGAAAAA 3 24 1 TTTCTCCACA 0.969923 -94 TTTCCTCACCTCCGTATTCT 7 24 0 TTTCCTCACC 0.949683 -10 CTCTGTTGCTTATTTTCACAATGA 11 5 0 TATTTTCACA 0.687988 -232 CATTCAACCCTTTATTCACTTTAATGTAAA 11 80 0 TTTATTCACT 0.756687 -157 TATTAAGAAATTTCTCCGCCCCGGATTGAT 12 21 1 TTTCTCCGCC 0.826291 -95 ATTCTCCACCCCATCATTAT 12 106 0 ATTCTCCACC 0.86033 -10 ATACACGATCTATATTCACAA 15 2 0 TATATTCACA 0.687988 -186 ATACACTTTATTTCTTCACAGAAAAGCCCC 15 45 1 TTTCTTCACA 0.984587 -143 ACATACAGAAATTCTTCACTTTGTTGGACA 16 124 1 ATTCTTCACT 0.804801 -177 TTTATTATCATTTCTTCACAGTTCAGTCTG 16 244 0 TTTCTTCACA 0.984587 -57 ********** Masking position 3 Map Score: 11.0572 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 592 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 TGATATAAGCCTGAAAATAGCAGAATTTCTG 1 93 0 CTGAAATAGC 0.872626 -208 ATTTCTCGCCCTGATATAAGCCTGAAAATAG 1 104 0 CTGTATAAGC 0.965241 -197 ACGGGTTCTGCCGCTAAAAACATGAAAAGTA 4 40 1 CCGTAAAAAC 0.935219 -121 CTGCTAAAAGCTGATCTTCAG 4 150 0 CTGTAAAAGC 0.991194 -11 GCTGTCCCCGCTGTTAAAAGCAAATGCTCGC 13 15 1 CTGTAAAAGC 0.991193 -148 CACATATGCCCCGCTAAAAGCAAAGTGAATG 15 123 0 CCGTAAAAGC 0.989397 -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 AGTCTTTCTATGTAATAATTTTAAT 1 3 1 TTTTCTTTAA 0.61324 -298 AAATTTTGCATTTTTCTTCAAAAAGTTTCAAAA 1 36 1 TTTTCTCAAA 0.789263 -265 GCGAGAAATGTAGTTCTAACAATCTAGGACTTT 1 126 1 TGTTCTAAAT 0.901832 -175 TTATGCCTGTTATTTCTTACAATAAGCATATAG 1 218 1 TTTTCTAAAT 0.959897 -83 GTCATTCCACTCTTTCTCTAAATCGTCAGACCC 2 12 0 TTTTCTTAAT 0.915528 -34 TTCCCTTTCCTTGTTCTGAAAGTTCCTTCAATC 4 108 0 TGTTCTAAGT 0.709055 -53 AATCGTAACATCTTTCTGATAATTAATCAATCC 12 43 0 TTTTCTAAAT 0.959824 -73 AATTCACATTTATTTCTTAATCTATGTATGAGT 13 120 0 TTTTCTATCT 0.808745 -43 CAGAGTGCAGTTTTTCTTAAAAAGCCGTTTAAT 16 163 1 TTTTCTAAAA 0.92778 -138 CGTTTAATTGTCTTTCTCTTACTTGCTCTCATT 16 188 1 TTTTCTTACT 0.885281 -113 TGCTCTCATTTTTTTCTGAGACAGGTTTAGAAT 16 211 1 TTTTCTAACA 0.900056 -90 * ***** * *** Masking position 7 Map Score: 5.53356 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 267 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 ACAAGGATATTGAGGGTGAAAAAAACTGAA 1 265 1 TGAGGGTGAA 0.863827 -36 CTCACCTTTTGCAGGCTGAAGAGAACCCGG 3 91 1 GCAGGCTGAA 0.944814 -27 AATAGCGCATTCAGTGTAAAGGGCTGCCCG 6 73 0 TCAGTGTAAA 0.837734 -179 TCATTGTGAAAATAAGCAAC 11 1 1 TCATTGTGAA 0.854667 -236 GGGTTGAATGGCAGTGTGCATCAGACCTCT 11 100 1 GCAGTGTGCA 0.970709 -137 ATTTCGGTGTGCAGTGTGAAAGCCTATACA 12 73 1 GCAGTGTGAA 0.985465 -43 CCCGCTAAAAGCAAAGTGAATGCCCTGTCA 15 115 0 GCAAAGTGAA 0.853254 -73 CAAACATTCCTCAGAGTGCAGTTTTTCTTA 16 152 1 TCAGAGTGCA 0.951851 -149 AGGTTTAGAATCAGACTGAACTGTGAAGAA 16 233 1 TCAGACTGAA 0.924918 -68 ********** Masking position 7 Map Score: 5.81123 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 218 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 GTTTTTTCTCCTTTCTTTTCGGCATTTTTG 1 64 0 CTTTCTTTTC 0.892119 -237 AGCAGAATTTCTGTTTTTTCTCCTTTCTTT 1 76 0 CTGTTTTTTC 0.974483 -225 ATTGTGAGGACATTTTTTTACACGAACTTC 1 181 1 CATTTTTTTA 0.798772 -120 GACTTTATGCCTGTTATTTCTTACAATAAG 1 214 1 CTGTTATTTC 0.895361 -87 ACCTCCATTTCAGTTTTTTTCACCCTCAAT 1 273 0 CAGTTTTTTT 0.815971 -28 GCTGTTTTTTCTCTCCTTTTA 9 22 0 CTGTTTTTTC 0.974483 -11 GGTTTTTGTTCTGTTTTGTAAAGGTTTACA 11 56 1 CTGTTTTGTA 0.649104 -181 CCCAGTCTCGCTGTCTTTTTGTCCTAGTAT 11 208 0 CTGTCTTTTT 0.722706 -29 ACAGCCAATTCTTTTTTTTATGCTATAATG 13 61 1 CTTTTTTTTA 0.870675 -102 CCCAAATTCACATTTATTTCTTAATCTATG 13 127 0 CATTTATTTC 0.759157 -36 AACGAATATTCCTTTTTTTCCTTTTTTCAT 16 13 0 CCTTTTTTTC 0.863715 -288 TACTTGCTCTCATTTTTTTCTGAGACAGGT 16 207 1 CATTTTTTTC 0.933636 -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 7 AAAAAGTTTCAAAAATGCCGAAAAGAAAGG 1 55 1 AAAAATGCCG 0.856241 -246 ATTGAGGGTGAAAAAAACTGAAATGGAGGT 1 273 1 AAAAAAACTG 0.79109 -28 TATTTTTCGGTAGAAAGCTGCGATCTTTTC 6 194 0 TAGAAAGCTG 0.846991 -58 TAAAATCAGCTGAAAAGCTGATTTTTTTAT 11 146 1 TGAAAAGCTG 0.968257 -91 ATTTCTTCACAGAAAAGCCCCTTTCTAAGG 15 54 1 AGAAAAGCCC 0.945084 -134 TCTTGAAATATGAAAAGCCCCTTAGAAAGG 15 73 0 TGAAAAGCCC 0.95496 -115 GTAACACATATAAAAAGCCATATCAAGCAT 16 91 0 TAAAAAGCCA 0.85791 -210 CGGCTTTTTAAGAAAAACTGCACTCTGAGG 16 160 0 AGAAAAACTG 0.829794 -141 CAGTTTTTCTTAAAAAGCCGTTTAATTGTC 16 170 1 TAAAAAGCCG 0.978969 -131 ********** Masking position 5 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 8 AATATATTCCCCCAGATGTTT 5 2 0 CCCAGATGTT 0.93819 -20 GTAATCGCTTCTCCGCTGTTTTATGATTAA 6 28 1 CTCCGCTGTT 0.987254 -224 AAATCAGCTTTTCAGCTGATTTTAGATCGT 11 140 0 TTCAGCTGAT 0.797581 -97 GCTGGCTGTCCCCGCTGTTAAAAGCAAAT 13 10 1 CCCCGCTGTT 0.994363 -153 GGCTGTATCCTCCCGCTGTTTGCGAGCATT 13 37 0 TCCCGCTGTT 0.987473 -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 9 TTTTTTTCACCCTCAATATCCTTGTCGAGA 1 260 0 CCTCAATATC 0.830617 -41 ATCCACTTACCTCCATTTCAGTTTTTTTC 1 282 0 CCTCCATTTC 0.967929 -19 CCCGGTCATTCCACTCTTTCTCTAAATCGT 2 19 0 CCACTCTTTC 0.917663 -27 AAACAAGAATCATCTATTTCTCCACAAAAG 3 18 1 CATCTATTTC 0.68187 -100 CGATTACTCGCCTCCCCTCCCTCC 6 5 0 CCTCCCCTCC 0.97872 -247 TCCGGTTCCTCTATTCCTTGATCCATT 6 235 0 CCTCTATTCC 0.949529 -17 TTTCCTCACCTCCGTATTCTGTC 7 21 0 CCTCACCTCC 0.953299 -13 ATTCTCCACCCCATCATTATGTATG 12 101 0 CCACCCCATC 0.862798 -15 ********** Masking position 4 Map Score: 2.81561 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 279 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 10 TTTCTTTTTTCCTTTTGTGGAGAAATAGATGA 3 27 0 CCTTTTGGAG 0.98451 -91 ATCATTCTCACCTTTTGCAGGCTGAAGAGAAC 3 85 1 CCTTTTGGGC 0.964156 -33 ATTAGCCGGACCTTTCGTCGAGACCGACGACG 4 11 1 CCTTTCGGAG 0.986951 -150 TTAAAGTAACCCGTTTGAACGGGCAGCCCTTT 6 54 1 CCGTTTGCGG 0.736878 -198 CCATTCGAGGAGGTGTCTCAC 10 1 1 CCATTCGGAG 0.939808 -21 CAGAAAAGCCCCTTTCTAAGGGGCTTTTCATA 15 63 1 CCTTTCTGGG 0.773174 -125 ATTCACTTTGCTTTTAGCGGGGCATATGTGCT 15 124 1 CTTTTAGGGG 0.846574 -64 CTGAATGTATCCTTTTGGGAGGAGGTGAAAGG 16 278 1 CCTTTTGAGG 0.953853 -23 ******* *** Masking position 5 Map Score: 2.33046 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 149 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 AAGCGCTCCGGGTTCTCTTCAGCCTGC 3 101 0 CTCCGTTCTC 0.978048 -17 TCGAGACCGACGACGGGTTCTGCCGCTAAAAA 4 28 1 CGACGTTCTG 0.961422 -133 GGAGTTCCCTTTCCTTGTTCTGAAAGTTCCTT 4 113 0 TTCCTTTCTG 0.910374 -48 GGAAAGGGAACTCCTAATTCTGAAGATCAGCT 4 131 1 CTCCTTTCTG 0.984998 -30 TTTCCTCACCTCCGTATTCTGTCAAATTATG 7 13 0 CTCCGTTCTG 0.99488 -21 CATATAACGCCGCCGGTTTTTGTTCTGTTTTG 11 42 1 CGCCGTTTTG 0.961422 -195 ***** ***** Masking position 8 Map Score: 2.46772 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 148 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 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 Motif number 13 ********** 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 14 ********** 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