AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -itrpR_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 CT165 300 hypothetical protein #2 CT167 55 hypothetical protein #3 CT168 65 hypothetical protein #4 trpR 55 Trp Operon Repressor #5 trpB 300 Tryptophan Synthase (Beta Chain) #6 trpC 196 Phosphoribosylanthranilate Isomerase #7 mrsA 245 Phosphoglucomutase #8 tyrP_1 51 Tyrosine Transport Motif number 1 TTTGAGCGGGATTTTTTTGTTTTCGTATTT 1 164 1 ATTTTTTTGT 0.955187 -137 TTGTTTTCGTATTTTTCTGTCCGCTTTTAT 1 180 1 ATTTTTCTGT 0.975386 -121 CTGTGAGGAATTTTCTCTTGTAGCAACA 1 283 0 AATTTTCTCT 0.894345 -18 TTAATGAACAAATATTCTGTTTTAGCAGTT 5 15 1 AATATTCTGT 0.862688 -286 TTTGCGCAGGATTATTCTGTCGCCAGTTTT 5 244 1 ATTATTCTGT 0.962008 -57 TTCTGTCGCCAGTTTTTTCTATGATTTTAA 5 258 1 AGTTTTTTCT 0.875665 -43 AACCTGTGCATGTATTTTGTAAGATAGATC 6 25 1 TGTATTTTGT 0.769596 -172 TTTTATATGATTTATTTTCTATTGCTTTGA 6 92 1 TTTATTTTCT 0.88225 -105 CTTGTCTTACTTTTTTCTGTGAATTTGCTT 6 149 1 TTTTTTCTGT 0.962008 -48 AAATGATTTATTTTTTTTGTTTTT 7 5 0 TTTTTTTTGT 0.9316 -241 GTTTTCGATAATTATTTTCTTACTTCTTAT 7 36 1 ATTATTTTCT 0.921418 -210 AATAGGGAATATTTATCTCTGAAAATCAAG 7 182 1 ATTTATCTCT 0.78404 -64 AATCTACAGTTTTTTCTCTCTTGATGAAT 8 10 1 TTTTTTCTCT 0.956139 -42 ********** Masking position 6 Map Score: 16.898 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 254 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 TTGGATTAGGAAAACTTCTTTATCAACTGGATTTC 1 89 0 AAAATCTTAA 0.945423 -212 AACCTTGTTGAAAACATCATAGAAAAGTGGCTCAA 1 122 1 AAAATCTAGA 0.927578 -179 CGTAATCACCAAAATTTCGTAAGGAACTATAAAAG 1 203 0 AAAATCTAAA 0.982085 -98 ACCTGTTAAAAACAAATCGTAATCACCAAAATTTC 1 220 0 AACATCTAAA 0.986029 -81 ATTTGTTTTTAACAGGTAATAACAAATACCCGTTC 1 238 1 AACATATAAA 0.873718 -63 GCATTGGGCGAAAAAGTCTCTAAGAAGAGGATCTC 3 12 1 AAAATCCTAA 0.801877 -54 ATAATATTACAACATTTCATAAATATATGCTACA 4 10 0 AACATCTAAA 0.986029 -46 CTTCTATAAGAACATCTCTTAATCAAATAAAAGGC 5 196 0 AACATCTAAA 0.986029 -105 GATGTTTGAGGAAAGGTCTTAAGAAGGCGAATTGC 7 132 1 GAAATCTAAA 0.927578 -114 **** ** *** * Masking position 7 Map Score: 8.30125 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 43 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 TTTTTTGTTTTCGTATTTTTCTGTCCGCTT 1 176 1 TCGTATTTTT 0.812756 -125 AGCGTGCCTGGCTTTCTTTTGAAAGCTGGC 5 133 1 GCTTTCTTTT 0.928389 -168 AAAAAGACGCTCTTACTTCTATAAGAACAT 5 216 0 TCTTACTTCT 0.972065 -85 TGCAAGGAAGGCTTATTTTTATATGATTTA 6 76 1 GCTTATTTTT 0.944553 -121 AATCTTCTTGTCTTACTTTTTTCTGTGAAT 6 143 1 TCTTACTTTT 0.981029 -54 ATAATTATTTTCTTACTTCTTATTTAAAAA 7 43 1 TCTTACTTCT 0.972065 -203 GGTATCAATAGCTTACTATTTATAACCAAA 7 96 0 GCTTACTATT 0.928389 -150 ********** Masking position 4 Map Score: 6.03854 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 25 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 TTTTTTGTTTTCGTATTTTTCTGTCCGCTT 1 176 1 TCGTATTTTT 0.664567 -125 GATTGATGCTTCCTCTGTTTTCTACTCCTA 2 19 0 TCCTCTGTTT 0.926801 -37 GAATGAGAGATCCTCTTCTTAGAGACTTTT 3 23 0 TCCTCTTCTT 0.892714 -43 ATCGCACCTTTTTGTAATGCTAT 4 43 0 GCACCTTTTT 0.88208 -13 AAGTAGATAAGCGCCAGCTTTCAAAAGAAA 5 145 0 GCGCCAGCTT 0.925184 -156 AGAAGTAAGAGCGTCTTTTTTGCGCAGGAT 5 226 1 GCGTCTTTTT 0.973092 -75 GATTATTCTGTCGCCAGTTTTTTCTATGAT 5 253 1 TCGCCAGTTT 0.915903 -48 GTTGGTTTTAGCCCCTTTGTTAT 6 184 1 GCCCCTTTGT 0.874117 -13 TCTTTGCAATTCGCCTTCTTAAGACCTTTC 7 142 0 TCGCCTTCTT 0.962614 -104 AATAGCATAAGCGTCTGTATCTTAG 8 37 1 GCGTCTGTAT 0.860653 -15 ********** Masking position 10 Map Score: 5.22163 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 242 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 TTATCAACTGGATTTCAATAAAACCTTAGT 1 75 0 GATTTCAATA 0.952101 -226 TTTCTATGATGTTTTCAACAAGGTTGGATT 1 117 0 GTTTTCAACA 0.969052 -184 ATTACGATTTGTTTTTAACAGGTAATAACA 1 232 1 GTTTTTAACA 0.952184 -69 TTTTTTCTATGATTTTAACACTATAATTTT 5 270 1 GATTTTAACA 0.952177 -31 AAATCATTTAGTTTTCGATAATTATTTTCT 7 26 1 GTTTTCGATA 0.942888 -220 GAATTGCAAAGATTTTGATAAAAATAGGGA 7 160 1 GATTTTGATA 0.913035 -86 ********** Masking position 5 Map Score: 4.53542 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 43 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 GTATAGCTGCAGCATGCCATGCAAATCAGCTT 5 56 1 AGCTGCCAGC 0.996528 -245 CATGCAAATCAGCTTTTCAAGCTGATTGCTTC 5 73 1 AGCTTTCAGC 0.979041 -228 ATCCTCTTACAGCGTGCCTGGCTTTCTTTTGA 5 123 1 AGCTGCCTGC 0.996528 -178 TATAAAAATAAGCCTTCCTTGCAAGAAATCGA 6 67 0 AGCTTCCTGC 0.994641 -130 *** ***** ** Masking position 5 Map Score: 2.18915 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 10 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 TGCAGCATGCCATGCAAATCAGCTTTTCAA 5 63 1 CATGCAAATC 0.834182 -238 AGGATGAATTTTTGAATATCTTGGAAGCAA 5 98 0 TTTGAATATC 0.825425 -203 CTTACTTCTATAAGAACATCTCTTAATCAA 5 205 0 TAAGAACATC 0.86269 -96 CACAGGTTATTCAGCAAATCTC 6 3 0 TCAGCAAATC 0.947302 -194 GACAAGAAGATTAGCATATCCAAGAGATTT 6 125 0 TTAGCATATC 0.882905 -72 ACCAACTATTTAAGCAAATTCACAGAAAAA 6 160 0 TAAGCAAATT 0.734988 -37 AAATAAGAAGTAAGAAAATAATTATCGAAA 7 38 0 TAAGAAAATA 0.673911 -208 TATCAAAATCTTTGCAATTCGCCTTCTTAA 7 150 0 TTTGCAATTC 0.640353 -96 TCCCTATTTTTATCAAAATCTTTGCAATTC 7 160 0 TATCAAAATC 0.699217 -86 AATATTTATCTCTGAAAATCAAGGATCAGT 7 189 1 TCTGAAAATC 0.918515 -57 GCTCTATCCCTAAGAATATCCTTTGGCTCA 7 225 0 TAAGAATATC 0.91461 -21 ********** Masking position 6 Map Score: 3.08471 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 227 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 AAAACCTTAGTGGATAGGAATCATACTTTCGA 1 54 0 TGGTAGAATC 0.977944 -247 CTTTATCAACTGGATTTCAATAAAACCTTAGT 1 75 0 TGGTTTAATA 0.805761 -226 TTTGAATATCTTGGAAGCAATCAGCTTGAAAA 5 86 0 TTGAAGAATC 0.91098 -215 TAAGCCTTCCTTGCAAGAAATCGAGTATTACG 6 59 0 TTGAAGAATC 0.91098 -138 TTCTATTGCTTTGATATAAATCTCTTGGATAT 6 108 1 TTGTATAATC 0.958589 -89 AATTTTTGTTTGGTTATAAATAGTAAGCTATT 7 88 1 TGGTATAATA 0.958556 -158 AACATCAATCTGGGTATCAATAGCTTACTATT 7 106 0 TGGTATAATA 0.958589 -140 TGCAAAGATTTTGATAAAAATAGGGAATATTT 7 164 1 TTGTAAAATA 0.816032 -82 *** *** **** Masking position 9 Map Score: 4.36835 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 9 TCCACTAAGGTTTTATTGAAATCCAGTTGATA 1 72 1 TTTATTGAAT 0.694145 -229 GGGATTTTTTTGTTTTCGTATTTTTCTGTCCG 1 171 1 TTTTTCGATT 0.828187 -130 ACATATTTTAGGAGTAGAAAACAGA 2 4 1 TTTTTAGAGT 0.938847 -52 AATGTTGTAATATTATAGCATTACAAAAAGGT 4 29 1 TTTATAGATT 0.961625 -27 ACAAATATTCTGTTTTAGCAGTTTTGGTACAT 5 22 1 TTTTTAGAGT 0.938856 -279 TTAAGAAGCCTTTTATTTGATTAAGAGATGTT 5 189 1 TTTATTTATT 0.750949 -112 TAAGAGATGTTCTTATAGAAGTAAGAGCGTCT 5 210 1 TTTATAGAGT 0.957863 -91 GTCGCCAGTTTTTTCTATGATTTTAACACTAT 5 262 1 TTTCTATATT 0.750554 -39 GAAGGCTTATTTTTATATGATTTATTTTCTAT 6 82 1 TTTATATATT 0.891667 -115 * ****** *** Masking position 6 Map Score: 2.97901 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 87 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 TTCCGAATCCGATTGTTGCTACAAGAGAAA 1 270 1 GATTGTTGCT 0.941894 -31 TCTACCTTAAGATTGATGCTTCCTCTGTTT 2 29 0 GATTGATGCT 0.981594 -27 ATTTTTATATGATTTATTTTCTATTGCTTT 6 90 1 GATTTATTTT 0.906817 -107 AAAACTAAATGATTTATTTTTTTTGTTTTT 7 11 0 GATTTATTTT 0.906817 -235 TTGATACCCAGATTGATGTTTGAGGAAAGG 7 118 1 GATTGATGTT 0.98016 -128 ********** Masking position 4 Map Score: 2.35613 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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: 1.21035e-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: 1.21035e-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 13 ********** No masking Map Score: 1.21035e-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