AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -iflhCD_aquae_opreg_100.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 fliQ 300 flagellar biosynthesis protein FliQ #4 aq_2013 74 hypothetical protein Motif number 1 CCGTAGTGGAGTTGAAACGTAATGAACA 3 6 1 GTGAGTGAAC 0.998555 -295 CTCCACTACGGTACATTAGGAACTGCTGGATTT 3 55 0 GTCATTGAAC 0.997189 -246 ATGTACCGTAGTGGAGTTGAAACGTAGAATTTC 3 72 1 GTGAGTGAAC 0.998555 -229 CTCCACTACGGTACATTAGGAACAAGTGAGGAG 3 121 0 GTCATTGAAC 0.997189 -180 ATGTACCGTAGTGGAGTTGAAACTGTATTTACA 3 138 1 GTGAGTGAAC 0.998555 -163 CTCCACTACGGTACATTAGGAACTTATTTAGCA 3 188 0 GTCATTGAAC 0.997189 -113 ATGTACCGTAGTGGAGTTGAAACTGACTTCGGA 3 205 1 GTGAGTGAAC 0.998555 -96 CTTCCACACGGTACATTAGGAACAAAGAAAATC 3 256 0 GTCATTGAAC 0.997189 -45 ** **** * *** Masking position 5 Map Score: 31.4634 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 0 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 AGGCAAGAAATTATAAGGGGCTTA 1 5 1 AAGAAATTAT 0.927441 -33 ACGAAGTTCTTGAATACCTG 2 1 1 ACGAAGTTCT 0.950166 -231 CTAAAACTTGAGGAAGTTCTTCCCCTCGGG 2 130 1 AGGAAGTTCT 0.989979 -102 TACACACACGAAGAACATATCTTTCCCGAG 2 154 0 AAGAACATAT 0.770342 -78 GATAAAGGAGAAGAAGTTTTACCTTTTGAT 2 186 1 AAGAAGTTTT 0.934315 -46 TTGGCGTAATTGGGACTTATCAAAAGGTAA 2 204 0 TGGGACTTAT 0.795872 -28 ACGGTACATTAGGAACTGCTGGATTTCCCT 3 51 0 AGGAACTGCT 0.932147 -250 GAAAGACATGAGGAAATTCTACGTTTCAAC 3 87 0 AGGAAATTCT 0.974817 -214 GCATTCAAAAAAGGAGTTCTTGTAAATACA 3 161 0 AAGGAGTTCT 0.947567 -140 ACGGTACATTAGGAACTTATTTAGCATTCA 3 184 0 AGGAACTTAT 0.980472 -117 TACCGTGTGGAAGAAGCTATGGTAAAAATC 3 276 1 AAGAAGCTAT 0.860296 -25 AGTGGAAATTTTAACTCAGTAT 4 63 0 TGGAAATTTT 0.703226 -12 ********** Masking position 5 Map Score: 14.9071 Number of sites scoring better than the average of aligned sites = 959 Number in coding regions = 900 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 TCTCGTCCTCCTTTACTTTGCACTTCCCGTA 2 60 1 CTTACTTTGC 0.830101 -172 GTCCCAATTACGCCAAGGTGCTCT 2 218 1 CCCAAGGTGC 0.977467 -14 TTTTAATGTTCATTACGTTTCAACTCCACTA 3 14 0 CTTACGTTTC 0.956746 -287 GTTTCAACTCCACTACGGTACATTAGGAACT 3 64 0 CCTACGGTAC 0.996905 -237 CATGAGGAAATTCTACGTTTCAACTCCACTA 3 80 0 TCTACGTTTC 0.847271 -221 GTTTCAACTCCACTACGGTACATTAGGAACA 3 130 0 CCTACGGTAC 0.996905 -171 GTTTCAACTCCACTACGGTACATTAGGAACT 3 197 0 CCTACGGTAC 0.996905 -104 ATAGCTTCTTCCACACGGTACATTAGGAACA 3 265 0 CACACGGTAC 0.965777 -36 ATATTAAAGACTTAAAGGTGCACGACTTTCT 4 22 1 CTAAAGGTGC 0.86143 -53 * ********* Masking position 5 Map Score: 12.6821 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 98 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 CGAGAACTACGAGGAGAGAAATGCCAACCT 2 35 0 GAGGAGAGAA 0.845178 -197 CAAAGTAAAGGAGGACGAGAACTACGAGGA 2 50 0 GAGGACGAGA 0.963516 -182 CCGTAATCCTGAGGGGCAGACTTCAAAGGC 2 86 1 GAGGGGCAGA 0.958527 -146 TATCTTTCCCGAGGGGAAGAACTTCCTCAA 2 137 0 GAGGGGAAGA 0.980881 -95 TGTAAGGATAAAGGAGAAGAAGTTTTACCT 2 180 1 AAGGAGAAGA 0.927277 -52 CCGTAGTGGAGTTGAAACGTAATGA 3 6 1 GTGGAGTTGA 0.985853 -295 ACATTAAAATAAGGAAGGGAAATCCAGCAG 3 36 1 AAGGAAGGGA 0.527248 -265 ATGTACCGTAGTGGAGTTGAAACGTAGAAT 3 72 1 GTGGAGTTGA 0.985853 -229 AGGAACAAGTGAGGAGATGGGAAAGACATG 3 107 0 GAGGAGATGG 0.978976 -194 ATGTACCGTAGTGGAGTTGAAACTGTATTT 3 138 1 GTGGAGTTGA 0.985853 -163 ATGTACCGTAGTGGAGTTGAAACTGACTTC 3 205 1 GTGGAGTTGA 0.985853 -96 ACTGACTTCGGAGGGCGTGGACATTTCTTG 3 226 1 GAGGGCGTGG 0.882231 -75 ********** Masking position 4 Map Score: 19.8557 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 647 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 AAGTTTTAGGTTTTTAGCTTTGAGCCTTTG 2 109 0 TTTTTAGCTT 0.950396 -123 AGGAGAAGAAGTTTTACCTTTTGATAAGTC 2 191 1 GTTTTACCTT 0.968143 -41 GGAACTGCTGGATTTCCCTTCCTTATTTTA 3 40 0 GATTTCCCTT 0.946187 -261 TTTCCTCATGTCTTTCCCATCTCCTCACTT 3 101 1 TCTTTCCCAT 0.946883 -200 ATTAGGAACTTATTTAGCATTCAAAAAAGG 3 177 0 TATTTAGCAT 0.930416 -124 ATAAAGATTTTTACCATAGCTTCTTCC 3 284 0 TTTTTACCAT 0.973444 -17 ********** Masking position 5 Map Score: 3.38195 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 456 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 TTCGTGTGTGTAAGGATAAAGGAGAAGAAG 2 172 1 TAAGGATAAA 0.814497 -60 CTACGGTACATTAGGAACTGCTGGATTTCC 3 53 0 TTAGGAACTG 0.959559 -248 CTACGGTACATTAGGAACAAGTGAGGAGAT 3 119 0 TTAGGAACAA 0.989926 -182 CTACGGTACATTAGGAACTTATTTAGCATT 3 186 0 TTAGGAACTT 0.941209 -115 ACACGGTACATTAGGAACAAAGAAAATCCA 3 254 0 TTAGGAACAA 0.989926 -47 TTAAGATAAACATATTAAAG 4 1 1 TTAAGATAAA 0.733552 -74 ********** Masking position 6 Map Score: 3.5819 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 59 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AATGTTCATTACGTTTCAACTCCACTACGG 3 11 0 ACGTTTCAAC 0.993875 -290 AGGAAATTCTACGTTTCAACTCCACTACGG 3 77 0 ACGTTTCAAC 0.993875 -224 CTTGTAAATACAGTTTCAACTCCACTACGG 3 143 0 CAGTTTCAAC 0.993875 -158 CCTCCGAAGTCAGTTTCAACTCCACTACGG 3 210 0 CAGTTTCAAC 0.993875 -91 ********** Masking position 5 Map Score: 8.05287 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 2 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 ********** No masking Map Score: -7.36532e-13 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 9 ********** No masking Map Score: -7.36532e-13 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: -7.36532e-13 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