AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imetJ_ecoli_opreg_100.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 TTATACGTCTGGATGTCTAAACTAGCATGAAT 1 66 0 GGATGTAAAC 0.995983 -38 TTAGACATCCAGACGTATAAAAACAGGAATCC 1 78 1 AGACGTAAAA 0.927925 -26 AAGCTCCCGGGGATGAATAAACTTGCCGCCTT 2 60 0 GGATGTAAAC 0.995983 -177 GTAAACATCTGGACGGCTAAAATCCTTCGTCT 2 146 0 GGACGTAAAA 0.989323 -91 CGCCAATTATGGATGTGTAAACATCTGGACGG 2 162 0 GGATGTAAAC 0.995983 -75 TTGTGTTAATGGACGTCAATACATCTGGACAT 3 64 1 GGACGAATAC 0.928458 -213 CAATACATCTGGACATCTAAACTTCTTTGCGT 3 80 1 GGACATAAAC 0.953731 -197 AAAAACTTCAGGATGGTAAGAAAAAGAAAATC 4 134 0 GGATGAAGAA 0.84266 -167 AAATCAGGGAAGATGAAAAAACTTCAGGATGG 4 150 0 AGATGAAAAC 0.924532 -151 CTTTACATCTGGACGTCTAAACGGATAGATGT 4 236 1 GGACGTAAAC 0.996531 -65 TAGAATATAAGAATGACTAAAAGGAGAGAAA 5 10 0 GAATGTAAAA 0.85162 -147 TCAGCTATCTGGATGTCTAAACGTATAAGCGT 5 114 1 GGATGTAAAC 0.995983 -43 ***** ***** Masking position 9 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 TTTTTATACGTCTGGATGTCTAAACTAGCAT 1 70 0 TCTGGATTCT 0.995793 -34 GTCGGGATTCCTGTTTTTATAC 1 92 0 TCGGGATCCT 0.963807 -12 TGTGTAAACATCTGGACGGCTAAAATCCTTC 2 150 0 TCTGGACGCT 0.993635 -87 CGTCAATACATCTGGACATCTAAACTTCTTT 3 77 1 TCTGGACTCT 0.995708 -200 ATATTTGCAGTCCGGTTTGCTTTGCATACCG 4 103 1 TCCGGTTGCT 0.947204 -198 CATCTTTACATCTGGACGTCTAAACGGATAG 4 233 1 TCTGGACTCT 0.995708 -68 TGGCAAATTTTCTGGTTATCTTCAGCTATCT 5 93 1 TCTGGTTTCT 0.988591 -64 TCTTCAGCTATCTGGATGTCTAAACGTATAA 5 111 1 TCTGGATTCT 0.995793 -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 ATGCTAGTTTAGACATCCAGACGTATAAAA 1 70 1 AGACATCCAG 0.996139 -34 GAAGGATTTTAGCCGTCCAGATGTTTACAC 2 150 1 AGCCGTCCAG 0.990884 -87 CCAGATGTTTACACATCCATAATTGGCGGT 2 166 1 ACACATCCAT 0.907122 -71 CCAGATGTATTGACGTCCATTAACACAATG 3 62 0 TGACGTCCAT 0.943738 -215 AAAGAAGTTTAGATGTCCAGATGTATTGAC 3 78 0 AGATGTCCAG 0.989429 -199 CTATCCGTTTAGACGTCCAGATGTAAAGAT 4 234 0 AGACGTCCAG 0.997562 -67 AGATAGCTGAAGATAACCAGAAAATTTGCC 5 94 0 AGATAACCAG 0.913609 -63 TTATACGTTTAGACATCCAGATAGCTGAAG 5 112 0 AGACATCCAG 0.996139 -45 ********** Masking position 9 Map Score: 17.2511 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 175 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TATGCCAATTCTTCAGGATGCGCCCGCGAA 1 35 1 CTTCAGGATG 0.951538 -69 CGGTCACTTACTTCAGTAAGCTCCCGGGGA 2 79 0 CTTCAGTAAG 0.829817 -158 GGCTAAAATCCTTCGTCTTTTAAATTTATG 2 134 0 CTTCGTCTTT 0.938125 -103 AAGTCCTTCACTTCGGCATGAATAATTTGC 2 215 0 CTTCGGCATG 0.987776 -22 ACTTAATCCTCTTCGTCAATAAATTGAGAC 3 252 0 CTTCGTCAAT 0.938012 -25 GATGAAAAAACTTCAGGATGGTAAGAAAAA 4 141 0 CTTCAGGATG 0.951538 -160 GGTTGACGCCCTTCGGCTTTTCCTTCATCT 4 208 1 CTTCGGCTTT 0.972624 -93 TCGGCTTTTCCTTCATCTTTACATCTGGAC 4 220 1 CTTCATCTTT 0.9419 -81 ACCTTACCTCATCAATCGCTTGTAGT 4 285 0 CCTCATCAAT 0.753183 -16 ACTTTCTCACCTTCAACATGCAGGCTCGAC 5 61 1 CTTCAACATG 0.918022 -96 TTCTGGTTATCTTCAGCTATCTGGATGTCT 5 102 1 CTTCAGCTAT 0.957261 -55 ********** Masking position 3 Map Score: 14.1541 Number of sites scoring better than the average of aligned sites = 1109 Number in coding regions = 1038 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 5 GCCAATTCTTCAGGATGCGCCCGCGAATAT 1 38 1 CAGGATGCGC 0.92707 -66 CGTATAAAAACAGGAATCCCGAC 1 91 1 CAGGAATCCC 0.937848 -13 AATAAACTTGCCGCCTTCCCTAAATTCAAA 2 47 0 CCGCCTTCCC 0.788964 -190 TCACTTACTTCAGTAAGCTCCCGGGGATGA 2 76 0 CAGTAAGCTC 0.878077 -161 TGGAGAAACGCAGCCAACGCACCATAAATT 2 112 1 CAGCCAACGC 0.960136 -125 GAGGAATATACAGTAACCGCCAATTATGGA 2 181 0 CAGTAACCGC 0.953938 -56 ACTGTATATTCCTCAAGCGCAAATTATTCA 2 197 1 CCTCAAGCGC 0.942844 -40 TGGGTACTGACCGTAAACCCGCATAGTTTA 3 204 0 CCGTAAACCC 0.95173 -73 GCCGGATTCGTCGTAAACGCTTAATCCGGC 4 46 0 TCGTAAACGC 0.769631 -255 ACCTTACCTCATCAATCGCTTGTAGTTAT 4 282 0 CATCAATCGC 0.906405 -19 ********** Masking position 8 Map Score: 4.81926 Number of sites scoring better than the average of aligned sites = 4212 Number in coding regions = 4033 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 6 CTAGTTTAGACATCCAGACGTATAAAAACAG 1 73 1 CTCCAGACGT 0.830032 -31 GATGAATAAACTTGCCGCCTTCCCTAAATTC 2 50 0 CTGCCGCCTT 0.974325 -187 GCAAATTATTCATGCCGAAGTGAAGGACTTT 2 215 1 CTGCCGAAGT 0.968421 -22 GTGTAATGCACCTGTCGGCGTGATAATGCAT 3 149 0 CTGTCGGCGT 0.95596 -128 CATAGTTTACCGTACAGGCGTTACCGTGACA 3 182 0 CTACAGGCGT 0.941295 -95 ATCATAGGATTAGGCCGGATTAAGCGTTTAC 4 33 1 TGGCCGGATT 0.723594 -268 CTTATTGCTTCTTGCCGGATTCGTCGTAAAC 4 58 0 CTGCCGGATT 0.993087 -243 GTTTGCTTTGCATACCGGATTTTCTTTTTCT 4 117 1 CTACCGGATT 0.970471 -184 GTTTTTTCATCTTCCCTGATTTTTCCTCACC 4 160 1 CTCCCTGATT 0.816347 -141 TCACCTTCAACATGCAGGCTCGACATTGGCA 5 67 1 CTGCAGGCTC 0.930978 -90 * ********* Masking position 3 Map Score: 6.72472 Number of sites scoring better than the average of aligned sites = 1660 Number in coding regions = 1496 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 7 CTAAACTAGCATGAATATTCGCGGGCGCAT 1 52 0 ATGAATATTC 0.893109 -52 CTCTAATTATATGTAAATCCTATGGATTTT 2 20 1 ATGTAAATCC 0.803253 -217 GCTCCCGGGGATGAATAAACTTGCCGCCTT 2 60 0 ATGAATAAAC 0.871495 -177 TTTGCGCTTGAGGAATATACAGTAACCGCC 2 190 0 AGGAATATAC 0.933364 -47 GCCTAATCCTATGATAATTCAATATATTTC 4 18 0 ATGATAATTC 0.721946 -283 TGGTAAGAAAAAGAAAATCCGGTATGCAAA 4 123 0 AAGAAAATCC 0.877423 -178 ATCAGGGAAGATGAAAAAACTTCAGGATGG 4 150 0 ATGAAAAAAC 0.937412 -151 AATGATGGTGAGGAAAAATCAGGGAAGATG 4 167 0 AGGAAAAATC 0.936743 -134 GTAAAGATGAAGGAAAAGCCGAAGGGCGTC 4 212 0 AGGAAAAGCC 0.96174 -89 GAAAGTTTCAAGGAAAAGACTACGTTAGAA 5 37 0 AGGAAAAGAC 0.954161 -120 ********** Masking position 7 Map Score: 8.47273 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 294 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 8 ********** 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 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