AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iflhCD_ecoli_bsub_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 flhB 201 putative part of export apparatus for flagellar proteins #2 tap 45 methyl-accepting chemotaxis protein IV, peptide sensor receptor #3 tar 144 methyl-accepting chemotaxis protein II, aspartate sensor receptor #4 motA 126 proton conductor component of motor; no effect on switching #5 flhD 300 regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor #6 fliA 300 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #7 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #8 fliL 104 flagellar biosynthesis #9 fliO 62 flagellar biosynthesis #10 flgB 300 flagellar basal-body rod protein #11 fliF 45 flagellar basal-body M-ring protein #12 fliH 117 flagellar assembly protein #13 fliK 160 fliK #14 flgE 21 flagellar hook protein #15 fliL 251 flagellar protein #16 fliM 33 flagellar motor switch protein #17 cheY 25 two-component response regulator #18 flhA 32 flagella-associated protein #19 cheW 21 cheW #20 sigD 22 RNA polymerase sigma-28 factor (sigma-D) Motif number 1 TTTGTATTGCCTGATGTGGCGTGACCACGTC 1 9 1 GCCGATGGGG 0.999191 -193 TTATCAGACCGCCTGATATGACGTGGTCACGCC 1 28 0 GCCGATAGAG 0.971564 -174 ATATCAGGCGGTCTGATAAGGCGATGACGCCGC 1 42 1 GTCGATAGGG 0.979226 -160 GTGTGCGTTTGTCGGATGCGGCGTCATCGCCTT 1 59 0 GTCGATGGGG 0.994772 -143 CGCACACTATGCTTGATGTGTGGCAGCAAAAGC 1 85 1 GCTGATGGTG 0.915742 -117 GGTCATTGCCGCCTGATGGGGAGCGTTG 2 28 1 GCCGATGGGG 0.999191 -18 GAAATAAAAAACCCGATGCGCAGATCATCGGGT 3 38 0 ACCGATGGCG 0.967368 -107 ACGCCAAATTGCCTGATGCGCTGCGCTTATCAG 6 24 1 GCCGATGGCG 0.997349 -277 ATTTTTGTAGGCCGGATAAGGCGTTTACGCCGC 6 93 1 GCCGATAGGG 0.996742 -208 GCTTTATGTTGCCGGATGCGGCGTAAACGCCTT 6 110 0 GCCGATGGGG 0.999191 -191 AAAAAACCCCGCCGGTGGCGGGGAAGCACGTTG 6 155 0 GCCGTGGGGG 0.967272 -146 *** **** ** * Masking position 5 Map Score: 29.2616 Number of sites scoring better than the average of aligned sites = 780 Number in coding regions = 249 Number in noncoding regions = 531 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 2 TATTGCCTGATGTGGCGTGACCACGTCATATCAG 1 15 1 TTGGCGACAC 0.947428 -187 GTTTGTCGGATGCGGCGTCATCGCCTTATCAGAC 1 52 0 TCGGCGACGC 0.998814 -150 ACGCTCCCCATCAGGCGGCAATGACCGCGTTAGT 2 20 0 TAGGCGATGA 0.765655 -26 AAAGCAGCGGTACGTCGTTACCGCTGCTGGAATG 4 30 0 TCGTCGACGC 0.995885 -97 TGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGG 4 70 0 TAGGCGACGC 0.992349 -57 ACCGGGGCTTCCCGGCGACATCACGGGGTGCGGT 5 244 1 CCGGCGACAC 0.948586 -57 CATCACGGGGTGCGGTGAAACCGCATAAAAATAA 5 262 1 TCGGTGACGC 0.9907 -39 TGTTGCCGGATGCGGCGTAAACGCCTTATCCGGC 6 103 0 TCGGCGACGC 0.998814 -198 AGACGCGGATTACGGTGCTACCTCTGACG 8 6 0 TCGGTGACTC 0.893541 -99 CTAATTATCCTGCGTCTTGAGCGCAACAAAGCGG 8 45 0 TCGTCTACGC 0.940967 -60 GCGGTCTTCCTGTGTCGCTACTGCTTATCGGCTA 8 76 0 TTGTCGATGC 0.881272 -29 CGCCGGTTTCTGCTGCGCCACTGCTGCAG 9 44 1 TCTGCGATGC 0.916945 -19 AGCCGGACCTTTCGTCGAGACCGACGACGGGTTC 13 14 1 TCGTCGACGA 0.968269 -147 * ***** * *** Masking position 10 Map Score: 21.7913 Number of sites scoring better than the average of aligned sites = 1144 Number in coding regions = 865 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 GTAAGGGGCAAAACAGGCGGGATTTAGGGCT 1 115 0 AAACAGGGGG 0.912139 -87 TGAAATAAAAAACCCGATGCGCAGATCATCG 3 41 0 AACCCGAGCG 0.845563 -104 TTGCTGATGCCACCCGCCGCGAAATTGAAAT 3 66 0 CACCCGCGCG 0.984882 -79 TTGGGGCAAAAAAAAGCAGCGGTACGTCGTT 4 45 0 AAAAAGCGCG 0.90039 -82 CCGGCGACATCACGGGGTGCGGTGAAACCGC 5 255 1 CACGGGGGCG 0.96615 -46 GTAGGCCTGATAAGCGCAGCGCATCAGGCAA 6 32 0 TAAGCGCGCG 0.842482 -269 GCTTCCCCGCCACCGGCGGGGTTTTTTTCTG 6 161 1 CACCGGCGGG 0.868576 -140 CATAATCAGCCACGAGGTGCGCG 7 202 1 CACGAGGGCG 0.985209 -13 GGCGCAGCAGAAACCGGCGCGGAAGATTGCA 9 32 0 AAACCGGGCG 0.97797 -31 ACTTTCTATACAAGAGGTGCGTATTGATCAT 12 59 1 CAAGAGGGCG 0.979253 -59 CTTCAGCCTGCAAAAGGTGAGAATGATCAAT 12 81 0 CAAAAGGGAG 0.895325 -37 GGCTGAAGAGAACCCGGAGCGCTT 12 104 1 AACCCGGGCG 0.984293 -14 TTTAATCATAAAACAGCGGAGAAGCGATTAC 15 28 0 AAACAGCGAG 0.876115 -224 CGAAACACAAGGAGAGAGATAGATT 17 6 1 CACAAGGGAG 0.923516 -20 TTTTTCGATTTAAAAGGAGAGAAAAAACAGC 18 12 1 TAAAAGGGAG 0.62746 -21 ******* *** Masking position 2 Map Score: 15.9594 Number of sites scoring better than the average of aligned sites = 1789 Number in coding regions = 1684 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 CTGATACGGTGAGGCGCAACATTCCAG 4 6 1 AGGGAGGCGC 0.812591 -121 ACGCGCGATTGGGGCAAAAAAAAGCAGCGGTA 4 52 0 GGGAAAAAAA 0.790534 -75 CCCGCCGGTGGCGGGGAAGCACGTTGCTGACA 6 149 0 GGGGAAGCAC 0.751321 -152 GGTAAATTCCAGGCAGAAAAAAACCCCGCCGG 6 173 0 AGCGAAAAAA 0.829001 -128 GGGTTTATTGGCGGATAGAAAAAAACGAAAGC 7 92 1 GGGTAGAAAA 0.629566 -123 GCGCAACAAAGCGGGGAAAAGACGCGGATTAC 8 27 0 GGGGAAAAGA 0.97239 -78 AGTTTCAAAAATGCCGAAAAGAAAGGAGAAAA 10 59 1 AGCGAAAAGA 0.874346 -242 GCCGAAAAGAAAGGAGAAAAAACAGAAATTCT 10 71 1 AGGGAAAAAA 0.955684 -230 GGCTTATATCAGGGCGAGAAATGTAGTTCTAA 10 113 1 AGGGAGAAAT 0.809835 -188 AAGGATATTGAGGGTGAAAAAAACTGAAATGG 10 267 1 AGGGAAAAAA 0.955684 -34 TTCTCCACAAAAGGAAAAAAGAAAACTTTCTA 12 35 1 AGGAAAAAGA 0.82641 -83 CACCTTTTGCAGGCTGAAGAGAACCCGGAGCG 12 93 1 AGCGAAGAGA 0.861372 -25 GGAGGGAGGGGAGGCGAGTAATCGCTT 15 6 1 GGGGAGGCGA 0.948399 -246 TCATAAAACAGCGGAGAAGCGATTACTCGCCT 15 22 0 GGGGAAGCGA 0.941701 -230 ACTCTGTCAAATGGTAAGAAGTTTGTAGTAAA 15 140 1 AGGAAGAAGT 0.484568 -112 ACAGAATACGGAGGTGAGGAAA 16 22 1 GGGGAGGAAA 0.961437 -12 TTCGATTTAAAAGGAGAGAAAAAACAGC 18 15 1 AGGGAGAAAA 0.960842 -18 * ** ******* Masking position 7 Map Score: 14.207 Number of sites scoring better than the average of aligned sites = 1277 Number in coding regions = 1063 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 5 AAGCCCTAAATCCCGCCTGTTTTGCCCCTT 1 114 1 TCCCGCCTGT 0.793823 -88 CCGATGATCTGCGCATCGGGTTTTTTATTT 3 40 1 GCGCATCGGG 0.746952 -105 TATTTCAATTTCGCGGCGGGTGGCATCAGC 3 65 1 TCGCGGCGGG 0.928086 -80 TAAAGTTTCCCCCCTCCTTGCCGATAACGA 3 97 1 CCCCTCCTTG 0.872991 -48 TACGTCGTTACCGCTGCTGGAATGTTGCGC 4 24 0 CCGCTGCTGG 0.955752 -103 TAACGACGTACCGCTGCTTTTTTTTGCCCC 4 44 1 CCGCTGCTTT 0.914604 -83 AATCGCAGCCCCCCTCCGTTGTATGTGCGT 5 69 1 CCCCTCCGTT 0.920525 -232 ATTGCCTGATGCGCTGCGCTTATCAGGCCT 6 31 1 GCGCTGCGCT 0.888921 -270 CAGAAAAAAACCCCGCCGGTGGCGGGGAAG 6 162 0 CCCCGCCGGT 0.961348 -139 GATAAACAGCCCTGCGTTATATGAGTTA 6 283 0 GCCCTGCGTT 0.878017 -18 CGCGCACCTCGTGGCTGATTA 7 204 0 GCGCACCTCG 0.714105 -11 GCACCGTAATCCGCGTCTTTTCCCCGCTTT 8 22 1 CCGCGTCTTT 0.739428 -83 GTGCAATCTTCCGCGCCGGTTTCTGCTGCG 9 31 1 CCGCGCCGGT 0.979987 -32 AAGCGCTCCGGGTTCTCTTCAG 12 106 0 GCGCTCCGGG 0.970679 -12 CTGGAAAAGATCGCAGCTTTCTACCGAAAA 15 191 1 TCGCAGCTTT 0.577766 -61 ********** Masking position 4 Map Score: 13.5694 Number of sites scoring better than the average of aligned sites = 4382 Number in coding regions = 4182 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 6 ACGACGTACCGCTGCTTTTTTTTGCCCCAA 4 46 1 GCTGCTTTTT 0.734208 -81 TCTGCTTATTGCAGCTTATCGCAACTATTC 5 196 1 GCAGCTTATC 0.874836 -105 CTATTCTAATGCTAATTATTTTTTACCGGG 5 220 1 GCTAATTATT 0.766498 -81 AGCGCATCAGGCAATTTGGCGTTGCCGTCA 6 16 0 GCAATTTGGC 0.668342 -285 AAGTTGAATTGCAATTTATTGAATTTGCAC 6 63 1 GCAATTTATT 0.843789 -238 AACATAAAGCGCAATTTGTCAGCAACGTGC 6 133 1 GCAATTTGTC 0.853644 -168 ATAACGCAGGGCTGTTTATC 6 291 1 GCTGTTTATC 0.949798 -10 TTTTTTTGTTGCTATTTAGCGCCTTTGTCT 7 61 0 GCTATTTAGC 0.838885 -154 CTGCTTATCGGCTAATTATCCTGCGTCTTG 8 60 0 GCTAATTATC 0.847243 -45 AAAACTCCTGGCTACTTTTCATGTTTTTAG 13 53 0 GCTACTTTTC 0.880758 -108 CACTGAATGCGCTATTTATTGAACAGATTG 15 87 1 GCTATTTATT 0.912383 -165 GCTGTTTTTTCTCTCCTTTT 18 23 0 GCTGTTTTTT 0.795068 -10 ********** Masking position 6 Map Score: 7.5638 Number of sites scoring better than the average of aligned sites = 740 Number in coding regions = 659 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 ACCCGATGATCTGCGCATCGGGTTTTTTAT 3 38 1 CTGCGCATCG 0.880961 -107 AAAGGTGGTTCTGCTTATTGCAGCTTATCG 5 187 1 CTGCTTATTG 0.975436 -114 CTGCTTATTGCAGCTTATCGCAACTATTCT 5 197 1 CAGCTTATCG 0.82171 -104 TGACCCGGGAGTGAGTCTTGTTCCACTTTG 7 158 1 GTGAGTCTTG 0.753565 -57 CACCTCGTGGCTGATTATGGACGGCGTTAT 7 191 0 CTGATTATGG 0.775159 -24 GCTAATTATCCTGCGTCTTGAGCGCAACAA 8 50 0 CTGCGTCTTG 0.968386 -55 TGTGTCGCTACTGCTTATCGGCTAATTATC 8 70 0 CTGCTTATCG 0.970374 -35 GTAAAACTATATGCTTATTGTAAGAAATAA 10 227 0 ATGCTTATTG 0.90082 -74 GGAGAAATAGATGATTCTTGTTTAATGATA 12 11 0 ATGATTCTTG 0.645977 -107 TATACAAGAGGTGCGTATTGATCATTCTCA 12 65 1 GTGCGTATTG 0.938352 -53 ********** Masking position 8 Map Score: 5.18021 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 572 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 TGATGCCACCCGCCGCGAAATTGAAATAAA 3 63 0 CGCCGCGAAA 0.824392 -82 CCCCCCTCCTTGCCGATAACGAGATCAACT 3 105 1 TGCCGATAAC 0.984365 -40 CGGATAATCATGCCGATAACTCATATAACG 6 267 1 TGCCGATAAC 0.984365 -34 TTTTTCTATCCGCCAATAAACCCGTTTTTT 7 85 0 CGCCAATAAA 0.860387 -130 TGTTCCACTTTGCCAATAACGCCGTCCATA 7 176 1 TGCCAATAAC 0.935068 -39 CAGGATAATTAGCCGATAAGCAGTAGCGAC 8 67 1 AGCCGATAAG 0.914262 -38 GTTTCAAAAATGCCGAAAAGAAAGGAGAAA 10 60 1 TGCCGAAAAG 0.899735 -241 CGACGGGTTCTGCCGCTAAAAACATGAAAA 13 38 1 TGCCGCTAAA 0.957759 -123 ********** Masking position 8 Map Score: 5.19578 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 386 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 GTATTGCCTGATGTGGCGTGACCACGTCAT 1 14 1 ATGTGGCGTG 0.940481 -188 CGTTTGTCGGATGCGGCGTCATCGCCTTAT 1 57 0 ATGCGGCGTC 0.98967 -145 CGCTGCTGGAATGTTGCGCCTCACCGTATC 4 13 0 ATGTTGCGCC 0.958577 -114 GTGACGAGTACAGTTGCGTCGATTTAGGAA 5 102 1 CAGTTGCGTC 0.830342 -199 ATGTTGCCGGATGCGGCGTAAACGCCTTAT 6 108 0 ATGCGGCGTA 0.936791 -193 TCGGCTAATTATCCTGCGTCTTGAGCGCAA 8 53 0 ATCCTGCGTC 0.955295 -52 GCGCAGCAGAAACCGGCGCGGAAGATTGCA 9 32 0 AACCGGCGCG 0.836921 -31 GCGCCGGTTTCTGCTGCGCCACTGCTGCAG 9 43 1 CTGCTGCGCC 0.971034 -20 ********** Masking position 6 Map Score: 3.5718 Number of sites scoring better than the average of aligned sites = 1447 Number in coding regions = 1192 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 10 CGCCGCATCCGACAAACGCACACTATGCTT 1 69 1 GACAAACGCA 0.886884 -133 GATTGGGGCAAAAAAAAGCAGCGGTACGTC 4 48 0 AAAAAAAGCA 0.758848 -79 ACGCATTATTGAAAATCGCAGCCCCCCTCC 5 56 1 GAAAATCGCA 0.96827 -245 AGCGACACAGGAAGACCGCAACAC 8 91 1 GAAGACCGCA 0.907302 -14 AACCGGCGCGGAAGATTGCACAGTAGCGTG 9 22 0 GAAGATTGCA 0.913193 -41 ACTTTTTGAAGAAAAATGCAAAATTTATTA 10 32 0 GAAAAATGCA 0.947925 -269 ATATAAGCCTGAAAATAGCAGAATTTCTGT 10 92 0 GAAAATAGCA 0.936608 -209 TCCACAAAAGGAAAAAAGAAAACTTTCTAT 12 38 1 GAAAAAAGAA 0.613951 -80 CTGTTCTGGAAAAGATCGCAGCTTTCTACC 15 186 1 AAAGATCGCA 0.789738 -66 GCTTTCTACCGAAAAATACAAATATTTGCA 15 206 1 GAAAAATACA 0.613951 -46 ********** Masking position 5 Map Score: 4.13454 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 533 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 11 GTCGCCAATCCTGGAAAGAGTATTAAGC 1 184 0 TCCTGGAAAG 0.839392 -18 AAGGCACCTTCCTGAAAACAAGTTGATCT 3 126 0 TCCTGAAAAC 0.870249 -19 GCGCGTTAACGCCTGACGACTGAACATCCT 4 78 1 GCCTGACGAC 0.864073 -49 TACCGGGGCTTCCCGGCGACATCACGGGGT 5 243 1 TCCCGGCGAC 0.969103 -58 AAACGCCTTATCCGGCCTACAAAAATGTGC 6 89 0 TCCGGCCTAC 0.895348 -212 CCAGAAATTATCCGGGAGACGAGA 7 5 0 TCCGGGAGAC 0.982519 -210 CAGGCTTATATCAGGGCGAGAAATGTAGTT 10 111 1 TCAGGGCGAG 0.767318 -190 TTTTGAAAACTCCTGGCTACTTTTCATGTT 13 58 0 TCCTGGCTAC 0.959228 -103 AATTGTAGTATCCGGAAAACATTCAATCTG 15 110 0 TCCGGAAAAC 0.914078 -142 ********** Masking position 9 Map Score: 2.72231 Number of sites scoring better than the average of aligned sites = 1003 Number in coding regions = 812 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 12 GACCACGTCATATCAGGCGGTCTGATAAGG 1 33 1 TATCAGGCGG 0.979019 -169 CAACGCTCCCCATCAGGCGGCAATGACCGC 2 26 0 CATCAGGCGG 0.978602 -20 TTCCCGGCGACATCACGGGGTGCGGTGAAA 5 252 1 CATCACGGGG 0.955348 -49 AATGAGGGGTTATTTGGGGGTTACAGGTAA 6 200 0 TATTTGGGGG 0.929194 -101 TACCAGAAATTATCCGGGAGACGAGA 7 7 0 TATCCGGGAG 0.862165 -208 TTCAGGCTTATATCAGGGCGAGAAATGTAG 10 109 1 TATCAGGGCG 0.962056 -192 AAACATCTGGGGGAATATATT 14 4 1 CATCTGGGGG 0.982527 -18 TTAAGGTATTAGGGGGATAACA 20 7 1 TATTAGGGGG 0.967914 -16 ********** Masking position 2 Map Score: 8.75505 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 132 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 ********** No masking Map Score: 4.16621e-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 TCATCGGGTTCATTTCAATTGAGGAAATCG 3 17 0 CATTTCAATT 0.909633 -128 TCGGGTTTTTTATTTCAATTTCGCGGCGGG 3 55 1 TATTTCAATT 0.660039 -90 TACCCATTTATGTTAAGTAATTGA 5 5 1 CATTTATGTT 0.779838 -296 TGTAAAGACCCATTTCTATTTGTAAGGACA 5 146 1 CATTTCTATT 0.929665 -155 TCTCCCGGATAATTTCTGGTAGCAAAGCCT 7 16 1 AATTTCTGGT 0.739562 -199 AAAATAGCAGAATTTCTGTTTTTTCTCCTT 10 81 0 AATTTCTGTT 0.902206 -220 CACTTACCTCCATTTCAGTTTTTTTCACCC 10 278 0 CATTTCAGTT 0.954462 -23 ********** Masking position 2 Map Score: 0.185131 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 118 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 ********** No masking Map Score: 4.16621e-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