AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iflhCD_ecoli_hinf_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 Motif number 1 TTTGTATTGCCTGATGTGGCGTGACCACGTC 1 9 1 GCCGATGGGG 0.999416 -193 TTATCAGACCGCCTGATATGACGTGGTCACGCC 1 28 0 GCCGATAGAG 0.979317 -174 ATATCAGGCGGTCTGATAAGGCGATGACGCCGC 1 42 1 GTCGATAGGG 0.984922 -160 GTGTGCGTTTGTCGGATGCGGCGTCATCGCCTT 1 59 0 GTCGATGGGG 0.996222 -143 CGCACACTATGCTTGATGTGTGGCAGCAAAAGC 1 85 1 GCTGATGGTG 0.937737 -117 GGTCATTGCCGCCTGATGGGGAGCGTTG 2 28 1 GCCGATGGGG 0.999416 -18 GAAATAAAAAACCCGATGCGCAGATCATCGGGT 3 38 0 ACCGATGGCG 0.976236 -107 ACGCCAAATTGCCTGATGCGCTGCGCTTATCAG 6 24 1 GCCGATGGCG 0.998086 -277 ATTTTTGTAGGCCGGATAAGGCGTTTACGCCGC 6 93 1 GCCGATAGGG 0.997647 -208 GCTTTATGTTGCCGGATGCGGCGTAAACGCCTT 6 110 0 GCCGATGGGG 0.999416 -191 AAAAAACCCCGCCGGTGGCGGGGAAGCACGTTG 6 155 0 GCCGTGGGGG 0.976165 -146 *** **** ** * Masking position 5 Map Score: 34.7642 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 CTGATATGACGTGGTCACGCCACATCAGGCA 1 18 0 GTGGTCCGCC 0.904841 -184 GTCGGATGCGGCGTCATCGCCTTATCAGACC 1 51 0 GCGTCACGCC 0.994125 -151 TCCCCATCAGGCGGCAATGACCGCGTTAGTA 2 19 0 GCGGCATGAC 0.923929 -27 TTCGCGGCGGGTGGCATCAGCAATAAAGTTT 3 74 1 GTGGCACAGC 0.822433 -71 CAAGTTGATCTCGTTATCGGCAAGGAGGGGG 3 106 0 TCGTTACGGC 0.823214 -39 CATTCCAGCAGCGGTAACGACGTACCGCTGC 4 30 1 GCGGTACGAC 0.98699 -97 CCCCAATCGCGCGTTAACGCCTGACGACTGA 4 70 1 GCGTTACGCC 0.99363 -57 GCTGCAATAAGCAGAACCACCTTTTTGGTTT 5 180 0 GCAGAACACC 0.730573 -121 TTATTTTTATGCGGTTTCACCGCACCCCGTG 5 265 0 GCGGTTCACC 0.866207 -36 GAGACTGACGGCAACGCCAAATTGCCTG 6 8 1 ACGGCACGCC 0.953147 -293 GCCGGATGCGGCGTAAACGCCTTATCCGGCC 6 102 0 GCGTAACGCC 0.974814 -199 TCAGCAACGTGCTTCCCCGCCACCGGCGGGG 6 151 1 GCTTCCCGCC 0.720052 -150 TGCGTTATATGAGTTATCGGCATGATTATCC 6 268 0 GAGTTACGGC 0.904363 -33 ATTATGGACGGCGTTATTGGCAAAGTGGAAC 7 177 0 GCGTTATGGC 0.926443 -38 CGTCAGAGGTAGCACCGTAATCCGCG 8 6 1 GAGGTACACC 0.884077 -99 TAGCCGATAAGCAGTAGCGACACAGGAAGAC 8 76 1 GCAGTACGAC 0.922941 -29 CTGCAGCAGTGGCGCAGCAGAAA 9 50 0 GCAGCATGGC 0.826912 -13 ****** **** Masking position 11 Map Score: 23.4758 Number of sites scoring better than the average of aligned sites = 5635 Number in coding regions = 5057 Number in noncoding regions = 578 Number of orfs with sites within 600 bp upstream = 242 Fraction of orfs with sites within 600 bp upstream = 0.0388693 Motif number 3 TGATAAGGCGATGACGCCGCATCCGACAAA 1 55 1 ATGACGCCGC 0.730592 -147 AATCCCGCCTGTTTTGCCCCTTACTCAAAC 1 122 1 GTTTTGCCCC 0.965655 -80 ACCATTGAACGCTTTGCGCTCTGGCATCAT 1 150 1 GCTTTGCGCT 0.777202 -52 ACTAACGCGGTCATTGCCGCCTGATGGGGA 2 20 1 TCATTGCCGC 0.741995 -26 TTTTATTTCAATTTCGCGGCGGGTGGCATC 3 62 1 ATTTCGCGGC 0.900267 -83 CAGCAATAAAGTTTCCCCCCTCCTTGCCGA 3 91 1 GTTTCCCCCC 0.94414 -54 CGCTGCTGGAATGTTGCGCCTCACCGTATC 4 13 0 ATGTTGCGCC 0.799843 -114 CAGCGGTACGTCGTTACCGCTGCTGGAATG 4 30 0 TCGTTACCGC 0.737195 -97 CCGCTGCTTTTTTTTGCCCCAATCGCGCGT 4 54 1 TTTTTGCCCC 0.938954 -73 TTTTACCGGGGCTTCCCGGCGACATCACGG 5 240 1 GCTTCCCGGC 0.946036 -61 TTTTTATGCGGTTTCACCGCACCCCGTGAT 5 263 0 GTTTCACCGC 0.877686 -38 AGGCAATTTGGCGTTGCCGTCAGTCTC 6 8 0 GCGTTGCCGT 0.882666 -293 GGATAAGGCGTTTACGCCGCATCCGGCAAC 6 106 1 TTTACGCCGC 0.87026 -195 TCAGCAACGTGCTTCCCCGCCACCGGCGGG 6 151 1 GCTTCCCCGC 0.96464 -150 TTCGTTTTTTTCTATCCGCCAATAAACCCG 7 91 0 TCTATCCGCC 0.506879 -124 AATCCGCGTCTTTTCCCCGCTTTGTTGCGC 8 29 1 TTTTCCCCGC 0.935023 -76 TTTCCCCGCTTTGTTGCGCTCAAGACGCAG 8 40 1 TTGTTGCGCT 0.621627 -65 GTGTTGCGGTCTTCCTGTGT 8 95 0 GTGTTGCGGT 0.823756 -10 ********** Masking position 7 Map Score: 16.5423 Number of sites scoring better than the average of aligned sites = 7751 Number in coding regions = 7246 Number in noncoding regions = 505 Number of orfs with sites within 600 bp upstream = 437 Fraction of orfs with sites within 600 bp upstream = 0.0701895 Motif number 4 AAATTGAAATAAAAAACCCGATGCGCAGATC 3 45 0 AAAAACCCGA 0.795896 -100 GGTGAGGCGCAACATTCCAGCAGCGGTAACG 4 18 1 AAATTCCAGC 0.83483 -109 ATTGGGGCAAAAAAAAGCAGCGGTACGTCGT 4 46 0 AAAAAGCAGC 0.920143 -81 CGCATTATTGAAAATCGCAGCCCCCCTCCGT 5 57 1 AAATCGCAGC 0.948792 -244 TGTAGGCCTGATAAGCGCAGCGCATCAGGCA 6 33 0 ATAGCGCAGC 0.680355 -268 CCAGGCAGAAAAAAACCCCGCCGGTGGCGGG 6 166 0 AAAACCCCGC 0.99502 -135 GTAACCCCCAAATAACCCCTCATTTCACCCA 6 206 1 AAAACCCCTC 0.929376 -95 TCGTCCGATTAAAAACCCTGCAGAAACGGAT 6 241 1 AAAACCCTGC 0.975212 -60 GATAAACAGCCCTGCGTTATATGAG 6 286 0 AAAGCCCTGC 0.944185 -15 TCTATCCGCCAATAAACCCGTTTTTTTGTTG 7 80 0 AAAAACCCGT 0.873035 -135 GCAAACTCGAAAAATTGACGCTCCCATTATT 7 127 0 AAATTGACGC 0.524494 -88 CCACTTTGCCAATAACGCCGTCCATAATCAG 7 180 1 AAAACGCCGT 0.946211 -35 TGATGAATAACCACGCTACTGTGCAA 9 6 1 AAAACCACGC 0.961946 -57 ** ******** Masking position 4 Map Score: 11.0938 Number of sites scoring better than the average of aligned sites = 1937 Number in coding regions = 1673 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 5 TTGTCGGATGCGGCGTCATCGCCTTATCAG 1 54 0 CGGCGTCATC 0.826477 -148 TATGCTTGATGTGTGGCAGCAAAAGCCCTA 1 92 1 GTGTGGCAGC 0.934082 -110 ATTTCGCGGCGGGTGGCATCAGCAATAAAG 3 72 1 GGGTGGCATC 0.93613 -73 ATACAACGGAGGGGGGCTGCGATTTTCAAT 5 63 0 GGGGGGCTGC 0.985849 -238 AACCAAAAAGGTGGTTCTGCTTATTGCAGC 5 181 1 GTGGTTCTGC 0.83887 -120 TTATTTTTTACCGGGGCTTCCCGGCGACAT 5 235 1 CCGGGGCTTC 0.949846 -66 TATTTTTATGCGGTTTCACCGCACCCCGTG 5 265 0 CGGTTTCACC 0.737343 -36 CCCGCCGGTGGCGGGGAAGCACGTTGCTGA 6 151 0 GCGGGGAAGC 0.840467 -150 GCATGATTATCCGTTTCTGCAGGGTTTTTA 6 250 0 CCGTTTCTGC 0.920148 -51 AGACTCACTCCCGGGTCAGCAAACTCGAAA 7 146 0 CCGGGTCAGC 0.983453 -69 TCTTCCGCGCCGGTTTCTGCTGCGCCACTG 9 37 1 CGGTTTCTGC 0.934527 -26 ********** Masking position 10 Map Score: 7.6671 Number of sites scoring better than the average of aligned sites = 2803 Number in coding regions = 2687 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 6 CTGCTGGAATGTTGCGCCTCACCGTATCAG 4 7 0 GTTGCTCACG 0.957789 -120 TCCAGCAGCGGTAACGACGTACCGCTGCTTTTTT 4 33 1 GTAACGTACG 0.781559 -94 TTTTGCCCCAATCGCGCGTTAACGCCTGACGACT 4 65 1 ATCGCTTACG 0.980036 -62 TGTGATCTGCATCACGCATTATTGAAAATCGCAG 5 43 1 ATCACTTATG 0.783618 -258 GGTTCTGCTTATTGCAGCTTATCGCAACTATTCT 5 193 1 ATTGCTTACG 0.990141 -108 TCTAATGCTAATTATTTTTTACCGGGGCTTCCCG 5 224 1 ATTATTTACG 0.789223 -77 TACAAGTTGAATTGCAATTTATTGAATTTGCACA 6 60 1 ATTGCTTATG 0.945536 -241 CCGTTTTTTTGTTGCTATTTAGCGCCTTTGTCTT 7 60 0 GTTGCTTACG 0.990893 -155 TTCCTGTGTCGCTACTGCTTATCGGCTAATTATC 8 70 0 GCTACTTACG 0.906397 -35 GGCGCGGAAGATTGCACAGTAGCGTGGTTATTCA 9 14 0 ATTGCGTACG 0.977366 -49 ***** *** ** Masking position 11 Map Score: 5.87618 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 596 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 GTGACCACGTCATATCAGGCGGTCTGATAAGG 1 31 1 CATATAGCGG 0.875889 -171 GAGTAAGGGGCAAAACAGGCGGGATTTAGGGC 1 116 0 CAAAAAGCGG 0.966223 -86 CAACGCTCCCCATCAGGCGGCAATGACCGC 2 26 0 CCCATAGCGG 0.767668 -20 CATTTCAATTGAGGAAATCGGGAGAA 3 5 0 GAGGAACGGG 0.655263 -140 ACCCGATGCGCAGATCATCGGGTTCATTTCAA 3 29 0 CAGATACGGG 0.950611 -116 GCTTCCCGGCGACATCACGGGGTGCGGTGAAA 5 250 1 GACATAGGGG 0.950616 -51 ATTAGTGGGTGAAATGAGGGGTTATTTGGGGG 6 210 0 GAAATAGGGT 0.756272 -91 TTTGCTACCAGAAATTATCCGGGAGACGAGA 7 10 0 GAAATACCGG 0.95353 -205 TAAATAGCAACAAAAAAACGGGTTTATTGGCG 7 73 1 CAAAAACGGG 0.966223 -142 AACGAAAGCACAAATAATGGGAGCGTCAATTT 7 115 1 CAAATAGGGA 0.811273 -100 ACAAAGCGGGGAAAAGACGCGGATTACGGTGC 8 22 0 GAAAAAGCGG 0.953808 -83 GTCTTGAGCGCAACAAAGCGGGGAAAAGACGC 8 34 0 CAACAACGGG 0.843435 -71 ***** * **** Masking position 7 Map Score: 5.873 Number of sites scoring better than the average of aligned sites = 569 Number in coding regions = 468 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 8 CATCGGGTTCATTTCAATTGAGGAAATCGG 3 16 0 ATTTCAATTG 0.908725 -129 CGGGTTTTTTATTTCAATTTCGCGGCGGGT 3 56 1 ATTTCAATTT 0.95671 -89 GTAAAGACCCATTTCTATTTGTAAGGACAT 5 147 1 ATTTCTATTT 0.939112 -154 TACAAGTTGAATTGCAATTTATTGAATTTG 6 60 1 ATTGCAATTT 0.959771 -241 CCGTTTTTTTGTTGCTATTTAGCGCCTTTG 7 64 0 GTTGCTATTT 0.88236 -151 ********** Masking position 7 Map Score: 0.773146 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 34 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 AAGGCACCTTCCTGAAAACAAGTTGAT 3 128 0 CTTCCTGAAA 0.946738 -17 GGGTTTTTTTCTGCCTGGAATTTACCTGTA 6 179 1 CTGCCTGGAA 0.957305 -122 TGCCTGGAATTTACCTGTAACCCCCAAATA 6 190 1 TTACCTGTAA 0.871886 -111 GTAGGCTTTGCTACCAGAAATTATCCGGGA 7 18 0 CTACCAGAAA 0.968801 -197 GTAGCAAAGCCTACCAGTAAGTCAATAAGA 7 34 1 CTACCAGTAA 0.967784 -181 ********** Masking position 2 Map Score: 0.772624 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 174 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 ********** No masking Map Score: 2.27617e-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: 2.27617e-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: 2.27617e-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