AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ityrR_ctra_opreg_100.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 aroA 169 Phosphoshikimate 1-carboxyl vinyltransferase #2 tyrB 187 Aromatic AA Aminotransferase #3 mrsA 245 Phosphoglucomutase #4 tyrP_1 51 Tyrosine Transport #5 tyrP_2 181 Tyrosine Transport Motif number 1 AAAAAAACATAAAATCTTTCAACAA 1 6 1 AACATAAAAT 0.898664 -164 AAAATCTTTCAACAAGATTAATTATAACAA 1 21 1 AACAAGATTA 0.918821 -149 TAATTATAACAACAAAATAAAATCCTTTTC 1 39 1 AACAAAATAA 0.977489 -131 TCCTTTTCATAACAAAAAAATAGAACTTAT 1 61 1 AACAAAAAAA 0.981651 -109 AAATCGTGTAAACATGATAACCTAGTTTCT 2 98 0 AACATGATAA 0.949466 -90 AAAAACAAAAAAAATAAATCATT 3 4 1 AACAAAAAAA 0.981651 -242 AATAAGAAGTAAGAAAATAATTATCGAAAA 3 37 0 AAGAAAATAA 0.863189 -209 TTTATAACCAAACAAAAATTCAAACGGCCA 3 78 0 AACAAAAATT 0.842329 -168 TTCCCCTATCAACATGAAAAAACAGGGGGA 5 157 1 AACATGAAAA 0.958588 -25 ********** Masking position 4 Map Score: 11.3155 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 180 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 CCTCAAACATCAATCTGGGTATCAATAGCTTACTATTTA 3 104 0 CTCTTAAAAC 0.995329 -142 GATAAATATTCCCTATTTTTATCAAAATCTTTGCAATTC 3 160 0 CTATTAAAAC 0.990399 -86 TGCTCTATCCCTAAGAATATCCTTTGGCTCA 3 225 0 CTATTAAAAC 0.9904 -21 CTACAGTTTTTTCTCTCTTGATGAATAGCATAAGCGTCT 4 14 1 TTCTGAAAAC 0.948974 -38 TTCATCATTTCGATCTGTTTACAAAAAGCTCGCATAAAG 5 49 0 CTCTTAAAAC 0.995325 -133 CCAATCTATACTATATGGAGAAAAACAACTAGCAAACAG 5 95 0 CTATGAAAAC 0.9858 -87 ATAGGGGAATCTTTCTCATTACGAAATACGATCCAATCT 5 127 0 CTCTTAAATC 0.977875 -55 * *** ** ** * * Masking position 11 Map Score: 7.64351 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 3 TACATTAGCTATTCATTTTTAACCTTTTTA 1 138 1 ATTCATTTTT 0.968558 -32 AAACTAAATGATTTATTTTTTTTGTTTTT 3 10 0 ATTTATTTTT 0.962276 -236 AAAATAAATCATTTAGTTTTCGATAATTAT 3 21 1 ATTTAGTTTT 0.975676 -225 TCAAACGGCCATTCACTTTTTAAATAAGAA 3 59 0 ATTCACTTTT 0.947561 -187 ATCAAGGATCAGTTAGTTTTGAGCCAAAGG 3 206 1 AGTTAGTTTT 0.964275 -40 TCAAGCTCGCATTCAGATTTCCTTTATGCG 5 28 1 ATTCAGATTT 0.909554 -154 ACTGTTTGCTAGTTGTTTTTCTCCATATAG 5 94 1 AGTTGTTTTT 0.840812 -88 ********** Masking position 1 Map Score: 5.40715 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 53 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 4 AATATCATGCAAAAAACTCTTCCGAAGACT 1 109 1 AAAAAACTCT 0.950352 -61 GATTTAGGACAACAAGCTGTCATCTTACTG 2 123 1 AACAAGCTGT 0.953578 -65 TTACTGGAAAAAAAGACAGTAAGCAGCAGT 2 147 1 AAAAGACAGT 0.914676 -41 ATCAAGAGAGAAAAAACTGTAGATT 4 6 0 AAAAAACTGT 0.978432 -46 ATCTGTTTACAAAAAGCTCGCATAAAGGAA 5 46 0 AAAAAGCTCG 0.896565 -136 AAAAACAACTAGCAAACAGTCGCGCTTTCA 5 84 0 AGCAAACAGT 0.878251 -98 TATCAACATGAAAAAACAGGGGGAGGAGG 5 163 1 AAAAAACAGG 0.95909 -19 ********** Masking position 4 Map Score: 3.51853 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 130 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 AAAACATAAAATCTTTCAACAAGATTAATT 1 14 1 ATCTTTCAAC 0.752911 -156 GGTTCGATCCCGCTATGCTCCAATTTCTGT 2 11 0 CGCTATGCTC 0.924423 -177 GGGATCGAACCGCTGACCTCAACAATGCCA 2 30 1 CGCTGACCTC 0.95334 -158 TAGGACAACAAGCTGTCATCTTACTGGAAA 2 127 1 AGCTGTCATC 0.975284 -61 CCTTCTTAAGACCTTTCCTCAAACATCAAT 3 129 0 ACCTTTCCTC 0.958457 -117 CAAACAGTCGCGCTTTCATCATTTCGATCT 5 72 0 CGCTTTCATC 0.986927 -110 AGAAAGATTCCCCTATCAACATGAAAAAAC 5 150 1 CCCTATCAAC 0.922957 -32 ********** Masking position 4 Map Score: 2.45834 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 159 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 GTTGAAAGATTTTATGTTTTTTT 1 4 0 TTTATGTTTT 0.798948 -166 TGAAAAGGATTTTATTTTGTTGTTATAATT 1 40 0 TTTATTTTGT 0.876888 -130 GGAAATAAGTTCTATTTTTTTGTTATGAAA 1 65 0 TCTATTTTTT 0.928269 -105 ACATTAGCTATTCATTTTTAACCTTTTTAG 1 139 1 TTCATTTTTA 0.810534 -31 ATGTCTATTTTCTAAAAAGGTTA 1 157 0 TCTATTTTCT 0.945553 -13 CCCGCTATGCTCCAATTTCTGT 2 3 0 TCCAATTTCT 0.780422 -185 AACTAAATGATTTATTTTTTTTGTTTTT 3 9 0 TTTATTTTTT 0.958589 -237 GTTTTCGATAATTATTTTCTTACTTCTTAT 3 36 1 ATTATTTTCT 0.782519 -210 CAAACGGCCATTCACTTTTTAAATAAGAAG 3 58 0 TTCACTTTTT 0.799274 -188 GAATGGCCGTTTGAATTTTTGTTTGGTTAT 3 75 1 TTGAATTTTT 0.825708 -171 TAACTGATCCTTGATTTTCAGAGATAAATA 3 191 0 TTGATTTTCA 0.851654 -55 TGTTTGCTAGTTGTTTTTCTCCATATAGTA 5 96 1 TTGTTTTTCT 0.747974 -86 ********** Masking position 7 Map Score: 6.34943 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 339 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 ********** No masking Map Score: -6.939e-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 8 AAGATCATACGAGGGAAATAAGTTCTATTTT 1 77 0 GAGGGAAAAA 0.989494 -93 TCAGTTGGTAGAGCGCAACAATGGCATTGTT 2 50 0 GAGCGCAAAA 0.976858 -138 CTAATACCCCGAGGGAAGAAACTAGGTTATC 2 82 1 GAGGGAAGAA 0.966644 -106 AGTTAGTTTTGAGCCAAAGGATATTCTTAGG 3 216 1 GAGCCAAAGA 0.954887 -30 TATTCATCAAGAGAGAAAAAACTGTAGATT 4 10 0 GAGAGAAAAA 0.983841 -42 TTTGTAAACAGATCGAAATGATGAAAGCGCG 5 63 1 GATCGAAAGA 0.922923 -119 ATACTATATGGAGAAAAACAACTAGCAAACA 5 96 0 GAGAAAAAAA 0.904024 -86 ******** ** Masking position 7 Map Score: 5.05528 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 80 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: -6.939e-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: -6.939e-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 11 ********** No masking Map Score: -6.939e-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