AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iphoB_ctra_opreg_300.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ytgA 300 Solute Protein Binding Family #2 phnP 28 predicted metal dependent hydrolase (histidinic triad) #3 artJ 68 Arginine Binding Protein #4 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #5 CT382.1 182 hypothetical protein Motif number 1 CCTTTAAAATAGAGTTTTTCTTATGATCCC 1 166 1 AGAGTTTTTC 0.811952 -135 AGGGGATCGTATACTTTTTCAAAGTATGTC 1 255 1 ATACTTTTTC 0.921928 -46 AAGGCCCCTTAATCGTTTTCTAAAA 2 6 0 AATCGTTTTC 0.962989 -23 ATTCTTATTTTTTTTAAGAATCATGT 3 7 1 ATTTTTTTTA 0.808519 -62 CATCATTAAACGTTCTCTTCTCTTCAA 4 8 1 AAACGTTCTC 0.918951 -129 TTCATTGAAAAATCTTTCTATTTCTTTTCT 4 55 1 AATCTTTCTA 0.790704 -82 TAGATTTGTTTTCCTTGTTTCTT 4 124 0 ATTTGTTTTC 0.936227 -13 ACTTTTGTTAAAATTTTTTCGCTATACCGC 5 38 0 AAATTTTTTC 0.926616 -145 AATTTTAACAAAAGTTTTTCTTTGTCTTCA 5 53 1 AAAGTTTTTC 0.94205 -130 CAATGAATTTAATGGTTTTAAATTAAATTG 5 81 1 AATGGTTTTA 0.911812 -102 TTTTAAATTAAATTGTTTTCATTTGAATTT 5 96 1 AATTGTTTTC 0.952852 -87 TTTAAGATCTATTTGTTTTAGTTTTATAAT 5 136 1 ATTTGTTTTA 0.853667 -47 ACAAAACACAATAGTTTCTATTATAAAACT 5 155 0 ATAGTTTCTA 0.703165 -28 ********** Masking position 1 Map Score: 14.952 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 447 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 2 ATTATTTAGAATTGTCTCTTCGAGATGAGA 1 23 1 ATTGTCTCTT 0.919065 -278 AAATCTAGCGCGTTTCTCATCTCGAAGAGA 1 37 0 CGTTTCTCAT 0.966575 -264 TTTAAAATAGAGTTTTTCTTATGATCCCAT 1 168 1 AGTTTTTCTT 0.933193 -133 ATTAAACGTTCTCTTCTCTTCAAGAGAAGA 4 15 1 CTCTTCTCTT 0.979848 -122 AAAAAACGCCCTCTTCTCTTGAAGAGAAGA 4 26 0 CTCTTCTCTT 0.979848 -111 GAAGAGGGCGTTTTTTTCATTGAAAAATCT 4 40 1 TTTTTTTCAT 0.721306 -97 CTTTCTATTTCTTTTCTCTTCCCTGTGTGT 4 68 1 CTTTTCTCTT 0.987282 -69 TTTTCCTTGTTTCTTCTCTTAACTCATGAA 4 109 0 TTCTTCTCTT 0.942626 -28 TTTTAACAAAAGTTTTTCTTTGTCTTCAAT 5 55 1 AGTTTTTCTT 0.933193 -128 AAAACACAATAGTTTCTATTATAAAACTAA 5 153 0 AGTTTCTATT 0.816288 -30 ATTTTCTCACAAAACACAAT 5 173 0 ATTTTCTCAC 0.818942 -10 ********** Masking position 5 Map Score: 14.719 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 457 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 3 CCTCCAAAAAAAGAACCTCGCTTATCGCAA 1 110 0 AAGAACCTCG 0.990868 -191 AGCCTCCTGTAAGGAGCTCCCCCTCCAAAA 1 131 0 AAGGAGCTCC 0.952877 -170 TTTAAAGGATACAAGCCTCCTGTAAGGAGC 1 144 0 ACAAGCCTCC 0.968484 -157 AAGAGCCTCCAGATAATCGA 1 291 0 AAGAGCCTCC 0.997199 -10 TGCTTTTAAGAGCCTCGCAATCATTTT 5 8 1 AAGAGCCTCG 0.995926 -175 ********** Masking position 8 Map Score: 5.25618 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 39 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TTCTAAATAATTTTAACAACTAA 1 4 0 TTTTAACAAC 0.949071 -297 GCAAAGATACTTTTAACAGAATGAATTTAT 1 84 0 TTTTAACAGA 0.968094 -217 AAAAACTCTATTTTAAAGGATACAAGCCTC 1 155 0 TTTTAAAGGA 0.895733 -146 TTTTAGAAAACGATTAAGGG 2 1 1 TTTTAGAAAA 0.856296 -28 CCAACATGATTCTTAAAAAAAATAAGAAT 3 10 0 TCTTAAAAAA 0.924793 -59 ATTGCGAGGCTCTTAAAAGCA 5 2 0 TCTTAAAAGC 0.946365 -181 AGCGAAAAAATTTTAACAAAAGTTTTTCTT 5 45 1 TTTTAACAAA 0.968632 -138 AACAAATAGATCTTAAAAAATAAAATTAAA 5 123 0 TCTTAAAAAA 0.924793 -60 ********** Masking position 5 Map Score: 9.08891 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 134 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 5 CGCTAGACCCGGCCTATCGCCACATGGGATCA 1 189 0 GGCTACGCCA 0.983933 -112 CGATAGGCCGGGTCTAGCGCCGATAGTAGAAA 1 202 1 GGCTACGCCG 0.996324 -99 GATCCCCTAAGGACAAAAACCAACCGATATTT 1 231 0 GGCAAAACCA 0.955006 -70 CTAACGGCAGGGACTATACCCAACATGATTCT 3 27 0 GGCTAACCCA 0.989234 -42 CCGACTCAATGGTCTAACGGCAGGGACTATAC 3 40 0 GGCTACGGCA 0.994262 -29 ** *** ***** Masking position 6 Map Score: 4.52816 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 5 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 6 ACTCTATTTTAAAGGATACAAGCCTCCTGTA 1 150 0 AAGGATACAA 0.885534 -151 AAGATTTTTCAATGAAAAAAACGCCCTCTTC 4 40 0 AAGAAAAAAA 0.929672 -97 GAGAAGAAACAAGGAAAACAAATCTA 4 121 1 AAGAAAACAA 0.990283 -16 CATTAAATTCATTGAAGACAAAGAAAAACTT 5 64 0 ATGAAGACAA 0.941897 -119 AAACAATTTAATTTAAAACCATTAAATTCAT 5 83 0 ATTAAAACCA 0.788198 -100 ATTAAATTCAAATGAAAACAATTTAATTTAA 5 98 0 AAGAAAACAA 0.990283 -85 TCTATTATAAAACTAAAACAAATAGATCTTA 5 138 0 AATAAAACAA 0.965279 -45 ** ******** Masking position 6 Map Score: 5.48528 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 128 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 7 GCGTTTCTCATCTCGAAGAGACAATTCTAA 1 28 0 TCTCGAAGAG 0.990037 -273 CGCCCTCTTCTCTTGAAGAGAAGAGAACGT 4 20 0 TCTTGAAGAG 0.991613 -117 TTCTCTTAACTCATGAACAGCAAATCATAC 4 96 0 TCATGAACAG 0.973285 -41 ********** Masking position 6 Map Score: 0.268386 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 34 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 8 ********** No masking Map Score: -3.95472e-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: -3.95472e-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: -3.95472e-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