AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -itrpR_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 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 0.95653 -137 TTGTTTTCGTATTTTTCTGTCCGCTTTTAT 1 180 1 ATTTTTCTGT 0.976139 -121 CTGTGAGGAATTTTCTCTTGTAGCAACA 1 283 0 AATTTTCTCT 0.897316 -18 TTAATGAACAAATATTCTGTTTTAGCAGTT 5 15 1 AATATTCTGT 0.866416 -286 TTTGCGCAGGATTATTCTGTCGCCAGTTTT 5 244 1 ATTATTCTGT 0.963154 -57 TTCTGTCGCCAGTTTTTTCTATGATTTTAA 5 258 1 AGTTTTTTCT 0.87909 -43 AACCTGTGCATGTATTTTGTAAGATAGATC 6 25 1 TGTATTTTGT 0.775192 -172 TTTTATATGATTTATTTTCTATTGCTTTGA 6 92 1 TTTATTTTCT 0.885517 -105 CTTGTCTTACTTTTTTCTGTGAATTTGCTT 6 149 1 TTTTTTCTGT 0.963154 -48 AAATGATTTATTTTTTTTGTTTTT 7 5 0 TTTTTTTTGT 0.933601 -241 GTTTTCGATAATTATTTTCTTACTTCTTAT 7 36 1 ATTATTTTCT 0.923693 -210 AATAGGGAATATTTATCTCTGAAAATCAAG 7 182 1 ATTTATCTCT 0.789382 -64 AATCTACAGTTTTTTCTCTCTTGATGAAT 8 10 1 TTTTTTCTCT 0.957455 -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 GAAATCCAGTTGATAAAGAAGTTTTCCTAATCCAA 1 89 1 TTAAGATTTT 0.950459 -212 TTGAGCCACTTTTCTATGATGTTTTCAACAAGGTT 1 122 0 TCTAGATTTT 0.934145 -179 CTTTTATAGTTCCTTACGAAATTTTGGTGATTACG 1 203 1 TTTAGATTTT 0.983796 -98 GAAATTTTGGTGATTACGATTTGTTTTTAACAGGT 1 220 1 TTTAGATGTT 0.987368 -81 GAACGGGTATTTGTTATTACCTGTTAAAAACAAAT 1 238 0 TTTATATGTT 0.884562 -63 GAGATCCTCTTCTTAGAGACTTTTTCGCCCAATGC 3 12 0 TTAGGATTTT 0.817601 -54 TGTAGCATATATTTATGAAATGTTGTAATATTAT 4 10 1 TTTAGATGTT 0.987368 -46 GCCTTTTATTTGATTAAGAGATGTTCTTATAGAAG 5 196 1 TTTAGATGTT 0.987368 -105 GCAATTCGCCTTCTTAAGACCTTTCCTCAAACATC 7 132 0 TTTAGATTTC 0.934145 -114 * *** ** **** Masking position 9 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 0.814831 -125 AGCGTGCCTGGCTTTCTTTTGAAAGCTGGC 5 133 1 GCTTTCTTTT 0.929294 -168 AAAAAGACGCTCTTACTTCTATAAGAACAT 5 216 0 TCTTACTTCT 0.972434 -85 TGCAAGGAAGGCTTATTTTTATATGATTTA 6 76 1 GCTTATTTTT 0.945266 -121 AATCTTCTTGTCTTACTTTTTTCTGTGAAT 6 143 1 TCTTACTTTT 0.981282 -54 ATAATTATTTTCTTACTTCTTATTTAAAAA 7 43 1 TCTTACTTCT 0.972434 -203 GGTATCAATAGCTTACTATTTATAACCAAA 7 96 0 GCTTACTATT 0.929294 -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 TTATCAACTGGATTTCAATAAAACCTTAGT 1 75 0 GATTTCAATA 0.950899 -226 TTTCTATGATGTTTTCAACAAGGTTGGATT 1 117 0 GTTTTCAACA 0.968259 -184 ATTACGATTTGTTTTTAACAGGTAATAACA 1 232 1 GTTTTTAACA 0.95098 -69 TTTTTTCTATGATTTTAACACTATAATTTT 5 270 1 GATTTTAACA 0.950973 -31 AAATCATTTAGTTTTCGATAATTATTTTCT 7 26 1 GTTTTCGATA 0.941463 -220 GAATTGCAAAGATTTTGATAAAAATAGGGA 7 160 1 GATTTTGATA 0.910937 -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 5 AAGCGGACAGAAAAATACGAAAACAAAAAA 1 176 0 AAAAATACGA 0.67923 -125 TAGGAGTAGAAAACAGAGGAAGCATCAATC 2 19 1 AAACAGAGGA 0.931187 -37 AAAAGTCTCTAAGAAGAGGATCTCTCATTC 3 23 1 AAGAAGAGGA 0.89892 -43 ATAGCATTACAAAAAGGTGCGAT 4 43 1 AAAAAGGTGC 0.888825 -13 TTTCTTTTGAAAGCTGGCGCTTATCTACTT 5 145 1 AAGCTGGCGC 0.92966 -156 ATCCTGCGCAAAAAAGACGCTCTTACTTCT 5 226 0 AAAAAGACGC 0.97478 -75 ATCATAGAAAAAACTGGCGACAGAATAATC 5 253 0 AAACTGGCGA 0.920887 -48 ATAACAAAGGGGCTAAAACCAAC 6 184 0 ACAAAGGGGC 0.881256 -13 GAAAGGTCTTAAGAAGGCGAATTGCAAAGA 7 142 1 AAGAAGGCGA 0.964936 -104 CTAAGATACAGACGCTTATGCTATT 8 37 0 ATACAGACGC 0.868441 -15 ********** Masking position 1 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 6 ACTTTCGACCGCAAATGTCATTGTGGTTGTAGAT 1 28 0 GCAATGCTTT 0.967886 -273 AATACCCGTTCCGAATCCGATTGTTGCTACAAGA 1 262 1 CCAATCGTTT 0.953912 -39 AGCATGCCATGCAAATCAGCTTTTCAAGCTGATT 5 66 1 GCAATCGTTT 0.989044 -235 TCTTGGATATGCTAATCTTCTTGTCTTACTTTTT 6 130 1 GCAATCTTTT 0.970673 -67 AATTCAAACGGCCATTCACTTTTTAAATAAGAAG 7 58 0 GCATTCCTTT 0.98601 -188 CAAAATCTTTGCAATTCGCCTTCTTAAGACCTTT 7 143 0 GCATTCCTTT 0.986008 -103 ** **** * ** * Masking position 6 Map Score: 2.24527 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 29 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 AAGCTGATTTGCATGGCATGCTGCAGCTATAC 5 56 0 GCTGGCAGCT 0.996395 -245 GAAGCAATCAGCTTGAAAAGCTGATTTGCATG 5 73 0 GCTGAAAGCT 0.978251 -228 TCAAAAGAAAGCCAGGCACGCTGTAAGAGGAT 5 123 0 GCAGGCAGCT 0.996395 -178 TCGATTTCTTGCAAGGAAGGCTTATTTTTATA 6 67 1 GCAGGAAGCT 0.994435 -130 ** ***** *** Masking position 8 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 8 AAAACCTTAGTGGATAGGAATCATACTTTCGA 1 54 0 TGGTAGAATC 0.978788 -247 CTTTATCAACTGGATTTCAATAAAACCTTAGT 1 75 0 TGGTTTAATA 0.811926 -226 TTTGAATATCTTGGAAGCAATCAGCTTGAAAA 5 86 0 TTGAAGAATC 0.914161 -215 TAAGCCTTCCTTGCAAGAAATCGAGTATTACG 6 59 0 TTGAAGAATC 0.914161 -138 TTCTATTGCTTTGATATAAATCTCTTGGATAT 6 108 1 TTGTATAATC 0.960143 -89 AATTTTTGTTTGGTTATAAATAGTAAGCTATT 7 88 1 TGGTATAATA 0.960109 -158 AACATCAATCTGGGTATCAATAGCTTACTATT 7 106 0 TGGTATAATA 0.960143 -140 TGCAAAGATTTTGATAAAAATAGGGAATATTT 7 164 1 TTGTAAAATA 0.821942 -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 TGTTTTCTACTCCTAAAATATGT 2 3 0 TCCTAAATAT 0.938006 -53 CTTTTTGTAATGCTATAATATTACAACATTT 4 28 0 TGCTTAATAT 0.938509 -28 GTACCAAAACTGCTAAAACAGAATATTTGTT 5 21 0 TGCTAAACAG 0.966646 -280 CAAAAATTCATCCTCTTACAGCGTGCCTGGC 5 114 1 TCCTTTACAG 0.806968 -187 TATTTTCTATTGCTTTGATATAAATCTCTTG 6 104 1 TGCTTGATAT 0.848041 -93 TCTGTGAATTTGCTTAAATAGTTGGTTTTAG 6 164 1 TGCTAAATAG 0.959999 -33 TTAAGACCTTTCCTCAAACATCAATCTGGGT 7 123 0 TCCTAAACAT 0.94811 -123 **** ****** Masking position 8 Map Score: 1.59516 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 70 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 TGCAGCATGCCATGCAAATCAGCTTTTCAA 5 63 1 CATGCAAATC 0.847175 -238 AGGATGAATTTTTGAATATCTTGGAAGCAA 5 98 0 TTTGAATATC 0.838972 -203 CTTACTTCTATAAGAACATCTCTTAATCAA 5 205 0 TAAGAACATC 0.873787 -96 CACAGGTTATTCAGCAAATCTC 6 3 0 TCAGCAAATC 0.951942 -194 GACAAGAAGATTAGCATATCCAAGAGATTT 6 125 0 TTAGCATATC 0.892572 -72 ACCAACTATTTAAGCAAATTCACAGAAAAA 6 160 0 TAAGCAAATT 0.753457 -37 AAATAAGAAGTAAGAAAATAATTATCGAAA 7 38 0 TAAGAAAATA 0.69487 -208 TATCAAAATCTTTGCAATTCGCCTTCTTAA 7 150 0 TTTGCAATTC 0.662388 -96 TCCCTATTTTTATCAAAATCTTTGCAATTC 7 160 0 TATCAAAATC 0.719227 -86 AATATTTATCTCTGAAAATCAAGGATCAGT 7 189 1 TCTGAAAATC 0.925491 -57 GCTCTATCCCTAAGAATATCCTTTGGCTCA 7 225 0 TAAGAATATC 0.921892 -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 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