AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imetJ_ecoli_opreg_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 metC 103 cystathionine beta-lyase (beta-cystathionase) #2 metR_metE 236 metR: regulator for metE and metH, metE: tetrahydropteroyltriglutamate methyltransferase #3 metJ 276 repressor of all met genes but metF #4 metF 300 5,10-methylenetetrahydrofolate reductase #5 metA 156 homoserine transsuccinylase Motif number 1 ATTCATGCTAGTTTAGACATCCAGACGTATAA 1 66 1 GTTTACATCC 0.996607 -38 GGATTCCTGTTTTTATACGTCTGGATGTCTAA 1 78 0 TTTTACGTCT 0.938476 -26 AAGGCGGCAAGTTTATTCATCCCCGGGAGCTT 2 60 1 GTTTACATCC 0.996607 -177 AGACGAAGGATTTTAGCCGTCCAGATGTTTAC 2 146 1 TTTTACGTCC 0.990974 -91 CCGTCCAGATGTTTACACATCCATAATTGGCG 2 162 1 GTTTACATCC 0.996607 -75 ATGTCCAGATGTATTGACGTCCATTAACACAA 3 64 0 GTATTCGTCC 0.938936 -213 ACGCAAAGAAGTTTAGATGTCCAGATGTATTG 3 80 0 GTTTATGTCC 0.960665 -197 GATTTTCTTTTTCTTACCATCCTGAAGTTTTT 4 134 1 TTCTTCATCC 0.863862 -167 CCATCCTGAAGTTTTTTCATCTTCCCTGATTT 4 150 1 GTTTTCATCT 0.935546 -151 ACATCTATCCGTTTAGACGTCCAGATGTAAAG 4 236 0 GTTTACGTCC 0.997071 -65 TTTCTCTCCTTTTAGTCATTCTTATATTCTA 5 10 1 TTTTACATTC 0.871799 -147 ACGCTTATACGTTTAGACATCCAGATAGCTGA 5 114 0 GTTTACATCC 0.996607 -43 ***** ***** Masking position 4 Map Score: 27.0605 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 131 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 ATGCTAGTTTAGACATCCAGACGTATAAAAA 1 70 1 AGAATCCAGA 0.995957 -34 GTATAAAAACAGGAATCCCGAC 1 92 1 AGGATCCCGA 0.965179 -12 GAAGGATTTTAGCCGTCCAGATGTTTACACA 2 150 1 AGCGTCCAGA 0.993884 -87 AAAGAAGTTTAGATGTCCAGATGTATTGACG 3 77 0 AGAGTCCAGA 0.995876 -200 CGGTATGCAAAGCAAACCGGACTGCAAATAT 4 103 0 AGCAACCGGA 0.949173 -198 CTATCCGTTTAGACGTCCAGATGTAAAGATG 4 233 0 AGAGTCCAGA 0.995876 -68 AGATAGCTGAAGATAACCAGAAAATTTGCCA 5 93 0 AGAAACCAGA 0.989034 -64 TTATACGTTTAGACATCCAGATAGCTGAAGA 5 111 0 AGAATCCAGA 0.995957 -46 *** ******* Masking position 1 Map Score: 18.1313 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 34 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 TTCGCGGGCGCATCCTGAAGAATTGGCATAA 1 34 0 CATCCGAAGA 0.966398 -70 CTAGTTTAGACATCCAGACGTATAAAAACAG 1 73 1 CATCCGACGT 0.995653 -31 GATGTGTAAACATCTGGACGGCTAAAATCCT 2 152 0 CATCTGACGG 0.992116 -85 GCAAATTATTCATGCCGAAGTGAAGGACTTT 2 215 1 CATGCGAAGT 0.981032 -22 GACGTCAATACATCTGGACATCTAAACTTCT 3 75 1 CATCTGACAT 0.965012 -202 TATGCATTATCACGCCGACAGGTGCATTACA 3 148 1 CACGCGACAG 0.885042 -129 TTTTTCTTACCATCCTGAAGTTTTTTCATCT 4 141 1 CATCCGAAGT 0.991494 -160 TTCATCTTTACATCTGGACGTCTAAACGGAT 4 231 1 CATCTGACGT 0.989873 -70 GTCGAGCCTGCATGTTGAAGGTGAGAAAGTT 5 60 0 CATGTGAAGG 0.966007 -97 TACGTTTAGACATCCAGATAGCTGAAGATAA 5 108 0 CATCCGATAG 0.92791 -49 ***** ***** Masking position 8 Map Score: 17.5654 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 489 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 AATTATATGTAAATCCTATGGATTTTGAATT 2 24 1 AAATCCTAGG 0.923194 -213 CATAAATTTAAAAGACGAAGGATTTTAGCCG 2 134 1 AAAGACGAGG 0.99315 -103 TTTCACCGACAAAGCCCAGGGAACTTCATCA 3 12 0 AAAGCCCAGG 0.991749 -265 GATGGTGAGGAAAAATCAGGGAAGATGAAAA 4 163 0 AAAAATCAGG 0.807704 -138 AGATGAAGGAAAAGCCGAAGGGCGTCAACCG 4 207 0 AAAGCCGAGG 0.994321 -94 GTCCAGATGTAAAGATGAAGGAAAAGCCGAA 4 219 0 AAAGATGAGG 0.975338 -82 GTTTCAAGGAAAAGACTACGTTAGAATATAA 5 32 0 AAAGACTAGT 0.893003 -125 ******** ** Masking position 8 Map Score: 6.3488 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 155 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 GAATTGGCATAAAGCAGAAAATTTTCGCAAA 1 15 0 AAGCAGAAAA 0.679884 -89 CTGGATGTCTAAACTAGCATGAATATTCGCG 1 59 0 AACTAGCATG 0.810452 -45 GAATTTAGGGAAGGCGGCAAGTTTATTCATC 2 50 1 AAGCGGCAAG 0.978592 -187 GGGGTGGAGAAACGCAGCCAACGCACCATAA 2 108 1 AAGCAGCCAA 0.884512 -129 TACTGACCGTAAACCCGCATAGTTTACCGTA 3 199 0 AACCCGCATA 0.928583 -78 GTAAACGCTTAATCCGGCCTAATCCTATGAT 4 33 0 AACCGGCCTA 0.978616 -268 GTTTACGACGAATCCGGCAAGAAGCAATAAG 4 58 1 AACCGGCAAG 0.989063 -243 TATGCAAAGCAAACCGGACTGCAAATATAAA 4 100 0 AACCGGACTG 0.954648 -201 AGAAAAAGAAAATCCGGTATGCAAAGCAAAC 4 117 0 AACCGGTATG 0.935343 -184 ** ******** Masking position 2 Map Score: 5.78496 Number of sites scoring better than the average of aligned sites = 1483 Number in coding regions = 1301 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 6 CCATTTGCGAAAATTTTCTGCTTTATGCCA 1 12 1 AAATTTTCTG 0.942802 -92 TTTCTTCCTCTAATTATATGTAAATCCTAT 2 13 1 TAATTATATG 0.952111 -224 CTTCGTCTTTTAAATTTATGGTGCGTTGGC 2 124 0 TAAATTTATG 0.830654 -113 ATAGCCGTTAAAATTATATGCATTATCACG 3 132 1 AAATTATATG 0.952111 -145 CAATCGCTTGTAGTTATATGTTGTGTTGTG 4 269 0 TAGTTATATG 0.879052 -32 CGACATTGGCAAATTTTCTGGTTATCTTCA 5 87 1 AAATTTTCTG 0.942802 -70 ********** Masking position 5 Map Score: 2.50803 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 87 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 TACATATAATTAGAGGAAGAAAAA 2 5 0 TAGAGGAAGA 0.873569 -232 TAATTTGCGCTTGAGGAATATACAGTAACC 2 193 0 TTGAGGAATA 0.871475 -44 GTGATGAAGTTCCCTGGGCT 3 1 1 GTGATGAAGT 0.940833 -276 TGCGTATAGATTGAGCAAATCCCAAATAGC 3 107 1 TTGAGCAAAT 0.777456 -170 TCTCAATTTATTGACGAAGAGGATTAAGTA 3 253 1 TTGACGAAGA 0.893912 -24 ACCAATGATGGTGAGGAAAAATCAGGGAAG 4 170 0 GTGAGGAAAA 0.95663 -131 CTACAAGCGATTGATGAGGTAAGGT 4 286 1 TTGATGAGGT 0.742649 -15 CATGTTGAAGGTGAGAAAGTTTCAAGGAAA 5 51 0 GTGAGAAAGT 0.885889 -106 AGCGTATGTAGTGAGGTAATCAGGTT 5 141 1 GTGAGGTAAT 0.810746 -16 ********** Masking position 4 Map Score: 2.13301 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 721 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 8 CCAATTCTTCAGGATGCGCCCGCGAATATT 1 39 1 AGGATGCGCC 0.960421 -65 CACTTACTTCAGTAAGCTCCCGGGGATGAA 2 75 0 AGTAAGCTCC 0.905061 -162 AGCTTACTGAAGTAAGTGACCGGGGTGGAG 2 87 1 AGTAAGTGAC 0.751288 -150 AGGAATATACAGTAACCGCCAATTATGGAT 2 180 0 AGTAACCGCC 0.969555 -57 CACGATGTCACGGTAACGCCTGTACGGTAA 3 177 1 CGGTAACGCC 0.919217 -100 CCGGATTCGTCGTAAACGCTTAATCCGGCC 4 45 0 CGTAAACGCT 0.817194 -256 GTAAAGATGAAGGAAAAGCCGAAGGGCGTC 4 212 0 AGGAAAAGCC 0.968343 -89 GAAAGTTTCAAGGAAAAGACTACGTTAGAA 5 37 0 AGGAAAAGAC 0.874943 -120 ********** Masking position 2 Map Score: 1.76421 Number of sites scoring better than the average of aligned sites = 1628 Number in coding regions = 1442 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 9 ********** No masking Map Score: 2.12695e-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 10 ********** No masking Map Score: 2.12695e-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 11 CATAAAGCAGAAAATTTTCGCAAATGGC 1 9 0 AAAATTTTCG 0.689561 -95 AACTAGCATGAATATTCGCGGGCGCATCCT 1 49 0 AATATTCGCG 0.781945 -55 GGGGATGAATAAACTTGCCGCCTTCCCTAA 2 54 0 AAACTTGCCG 0.959676 -183 TTACACATCCATAATTGGCGGTTACTGTAT 2 174 1 ATAATTGGCG 0.926613 -63 TTCGGCATGAATAATTTGCGCTTGAGGAAT 2 204 0 ATAATTTGCG 0.90747 -33 GACATCTAAACTTCTTTGCGTATAGATTGA 3 91 1 CTTCTTTGCG 0.920468 -186 GAGCAAATCCCAAATAGCCGTTAAAATTAT 3 119 1 CAAATAGCCG 0.879755 -158 CCTGTACGGTAAACTATGCGGGTTTACGGT 3 195 1 AAACTATGCG 0.912032 -82 GTACTTATTGCTTCTTGCCGGATTCGTCGT 4 62 0 CTTCTTGCCG 0.92325 -239 GTGTTGTGCACATCTATCCGTTTAGACGTC 4 247 0 CATCTATCCG 0.860985 -54 ********** Masking position 5 Map Score: 4.07493 Number of sites scoring better than the average of aligned sites = 1043 Number in coding regions = 940 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 12 ********** No masking Map Score: 2.12695e-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: 2.12695e-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 14 ********** No masking Map Score: 2.12695e-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