AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -iflhCD_aquae_opreg_300.orf -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 aq_1211 37 putative protein #2 fliP 231 flagellar biosynthetic protein FliP #3 aq_1922 24 hypothetical protein #4 fliQ 300 flagellar biosynthesis protein FliQ #5 aq_2013 74 hypothetical protein Motif number 1 TGTTCATTACGTTTCAACTCCACTACGG 4 6 0 GTTCATCCAC 0.998655 -295 AAATCCAGCAGTTCCTAATGTACCGTAGTGGAG 4 55 1 GTTCATGTAC 0.997831 -246 GAAATTCTACGTTTCAACTCCACTACGGTACAT 4 72 0 GTTCATCCAC 0.998655 -229 CTCCTCACTTGTTCCTAATGTACCGTAGTGGAG 4 121 1 GTTCATGTAC 0.997831 -180 TGTAAATACAGTTTCAACTCCACTACGGTACAT 4 138 0 GTTCATCCAC 0.998655 -163 TGCTAAATAAGTTCCTAATGTACCGTAGTGGAG 4 188 1 GTTCATGTAC 0.997831 -113 TCCGAAGTCAGTTTCAACTCCACTACGGTACAT 4 205 0 GTTCATCCAC 0.998655 -96 GATTTTCTTTGTTCCTAATGTACCGTGTGGAAG 4 256 1 GTTCATGTAC 0.997831 -45 *** * * ***** Masking position 7 Map Score: 31.301 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 4 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 CCTTTGAAGTCTGCCCCTCAGGATTACGGGA 2 84 0 CTCCCCTCAG 0.981929 -148 TGAGGAAGTTCTTCCCCTCGGGAAAGATATG 2 138 1 CTCCCCTCGG 0.997621 -94 TACGTTTCAACTCCACTACGG 4 1 0 CTCACTACGG 0.998485 -300 TACGTTTCAACTCCACTACGGTACATTAGGA 4 67 0 CTCACTACGG 0.998485 -234 ACAGTTTCAACTCCACTACGGTACATTAGGA 4 133 0 CTCACTACGG 0.998485 -168 TCAGTTTCAACTCCACTACGGTACATTAGGA 4 200 0 CTCACTACGG 0.998485 -101 ACCATAGCTTCTTCCACACGGTACATTAGGA 4 268 0 CTCCACACGG 0.992067 -33 ** ******** Masking position 2 Map Score: 22.0736 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 26 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 TTACGGGAAGTGCAAAGTAAAGGAGGACGAGA 2 60 0 TGAAAGTAAG 0.883177 -172 AGAGCACCTTGGCGTAATTGGGAC 2 218 0 AGACCTTGGG 0.913661 -14 GTAGTGGAGTTGAAACGTAATGAACATTAAAA 4 13 1 TGAACGTAAG 0.987185 -288 CAGTTCCTAATGTACCGTAGTGGAGTTGAAAC 4 63 1 TGACCGTAGG 0.99834 -238 GTAGTGGAGTTGAAACGTAGAATTTCCTCATG 4 79 1 TGAACGTAGA 0.950439 -222 TTGTTCCTAATGTACCGTAGTGGAGTTGAAAC 4 129 1 TGACCGTAGG 0.99834 -172 AAGTTCCTAATGTACCGTAGTGGAGTTGAAAC 4 196 1 TGACCGTAGG 0.99834 -105 TTGTTCCTAATGTACCGTGTGGAAGAAGCTAT 4 264 1 TGACCGTGTG 0.981391 -37 CAGAAAGTCGTGCACCTTTAAGTCTTTAATAT 5 22 0 TGACCTTTAG 0.905834 -53 ** ******* * Masking position 8 Map Score: 16.8632 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 41 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 AAGCCCCTTATAATTTCTTGCCT 1 2 0 TATTTCTTGC 0.872109 -36 ACGAAGTTCTTGAATACCTGCTAA 2 3 1 GAGTTCTTGA 0.981522 -229 CTAAAGGTTGGCATTTCTCTCCTCGTAGTTCT 2 31 1 GATTTCTCTC 0.93625 -201 TTCTCTCCTCGTAGTTCTCGTCCTCCTTTACT 2 45 1 GAGTTCTCGC 0.990328 -187 CCTTTACTTTGCACTTCCCGTAATCCTGAGGG 2 69 1 GACTTCCCGA 0.938154 -163 AAAACTTGAGGAAGTTCTTCCCCTCGGGAAAG 2 132 1 GAGTTCTTCC 0.98465 -100 TCAAAAGGTAAAACTTCTTCTCCTTTATCCTT 2 183 0 AACTTCTTCC 0.806574 -49 AGGAACTGCTGGATTTCCCTTCCTTATTTTAA 4 39 0 GATTTCCCTC 0.923559 -262 GGGAAATCCAGCAGTTCCTAATGTACCGTAGT 4 52 1 GAGTTCCTAT 0.752345 -249 TTGAAACGTAGAATTTCCTCATGTCTTTCCCA 4 88 1 GATTTCCTCT 0.883295 -213 ATTCAAAAAAGGAGTTCTTGTAAATACAGTTT 4 157 0 GAGTTCTTGA 0.981522 -144 GAGGGCGTGGACATTTCTTGGATTTTCTTTGT 4 236 1 AATTTCTTGA 0.836909 -65 * ******** * Masking position 3 Map Score: 11.488 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 932 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 GACGAGAACTACGAGGAGAGAAATGCCAACCTT 2 34 0 ACGAAAGAAA 0.95028 -198 TGCAAAGTAAAGGAGGACGAGAACTACGAGGAG 2 49 0 AGGAAGAGAA 0.969362 -183 TCTGCCCCTCAGGATTACGGGAAGTGCAAAGTA 2 73 0 AGGAAGGGAA 0.995134 -159 CGTGTGTGTAAGGATAAAGGAGAAGAAGTTTTA 2 174 1 AGGAAGGAGA 0.989035 -58 GGAACAAGTGAGGAGATGGGAAAGACATGAGGA 4 103 0 AGGATGGAAA 0.983834 -198 ACGGTACATTAGGAACAAAGAAAATCCAAGAAA 4 249 0 AGGAAAGAAA 0.988146 -52 **** * ***** Masking position 4 Map Score: 4.43606 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 308 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 AAGGCTCAAAGCTAAAAACCTAAAACTTGAG 2 111 1 GCTAAAACCT 0.939771 -121 TCTTTCCCGAGGGGAAGAACTTCCTCAAGTT 2 134 0 GGGGAAAACT 0.920513 -98 TCTTCCCCTCGGGAAAGATATGTTCTTCGTG 2 147 1 GGGAAAATAT 0.98073 -85 GTGAGGAGATGGGAAAGACATGAGGAAATTC 4 98 0 GGGAAAACAT 0.982124 -203 AAGAAGCTATGGTAAAAATCTTTAT 4 286 1 GGTAAAATCT 0.98073 -15 TTAAGATAAACATATTAAAGACTTA 5 5 1 GATAAAATAT 0.861152 -70 ****** **** Masking position 6 Map Score: 1.34751 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 126 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 GGCAAGAAATTATAAGGGGCTTAAAATAAT 1 12 1 TATAAGGGGC 0.950682 -26 GGACGAGAACTACGAGGAGAGAAATGCCAA 2 38 0 TACGAGGAGA 0.927822 -194 TTCCCGTAATCCTGAGGGGCAGACTTCAAA 2 83 1 CCTGAGGGGC 0.986727 -149 ACATATCTTTCCCGAGGGGAAGAACTTCCT 2 140 0 CCCGAGGGGA 0.990433 -92 GCTATTATTATACAAGGGGGTATT 3 5 0 TACAAGGGGG 0.977486 -20 GAAACTGACTTCGGAGGGCGTGGACATTTC 4 223 1 TCGGAGGGCG 0.945318 -78 ********** Masking position 5 Map Score: 1.9731 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 207 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 AGGCAAGAAATTATAAGGGG 1 1 1 AGGCAAGAAA 0.945113 -37 TTTAGCAGGTATTCAAGAACTTCGT 2 6 0 ATTCAAGAAC 0.979021 -226 GAAACTGTATTTACAAGAACTCCTTTTTTG 4 156 1 TTACAAGAAC 0.893758 -145 CTTATTTAGCATTCAAAAAAGGAGTTCTTG 4 169 0 ATTCAAAAAA 0.896942 -132 AACAAAGAAAATCCAAGAAATGTCCACGCC 4 239 0 ATCCAAGAAA 0.974261 -62 ********** Masking position 5 Map Score: 0.130696 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 51 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 9 ********** No masking Map Score: 1.69352e-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 10 ********** No masking Map Score: 1.69352e-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: 1.69352e-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