AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imetJ_ecoli_bsub_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 #6 metC 300 cobalamin-independent methionine synthase #7 metB 300 homoserine O-succinyltransferase Motif number 1 TTATACGTCTGGATGTCTAAACTAGCATGAAT 1 66 0 GGAGTTAAAC 0.98167 -38 TTAGACATCCAGACGTATAAAAACAGGAATCC 1 78 1 AGAGTTAAAA 0.87802 -26 ACATATAATTAGAGGAAGAAAAA 2 2 0 AGAGAGAAAA 0.900694 -235 AAGCTCCCGGGGATGAATAAACTTGCCGCCTT 2 60 0 GGAGATAAAC 0.98167 -177 TAAGTGACCGGGGTGGAGAAACGCAGCCAACG 2 99 1 GGGGGGAAAC 0.966204 -138 GTAAACATCTGGACGGCTAAAATCCTTCGTCT 2 146 0 GGAGGTAAAA 0.956562 -91 CGCCAATTATGGATGTGTAAACATCTGGACGG 2 162 0 GGAGTTAAAC 0.98167 -75 CAATACATCTGGACATCTAAACTTCTTTGCGT 3 80 1 GGAATTAAAC 0.891741 -197 CAGGATGGTAAGAAAAAGAAAATCCGGTATGC 4 126 0 AGAAAGAAAA 0.582466 -175 GAAAAATCAGGGAAGATGAAAAAACTTCAGGA 4 153 0 GGAGAGAAAA 0.962422 -148 TGACCAATGATGGTGAGGAAAAATCAGGGAAG 4 170 0 TGGGAGAAAA 0.60675 -131 CTTTACATCTGGACGTCTAAACGGATAGATGT 4 236 1 GGAGTTAAAC 0.98167 -65 TCAGCTATCTGGATGTCTAAACGTATAAGCGT 5 114 1 GGAGTTAAAC 0.98167 -43 TTACATATAAAGGAGGAGAAACA 6 288 1 AGGGGGAAAC 0.910108 -13 CTATACGTGTTGAGGGGGAAACAACAGAAAAC 7 208 0 TGAGGGAAAC 0.918456 -93 CCTATAATGAAGAAAATTAAACGGGGAAATAA 7 266 1 AGAAATAAAC 0.744706 -35 *** ** ***** Masking position 9 Map Score: 24.6265 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 575 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 2 TTTTTATACGTCTGGATGTCTAAACTAGCAT 1 70 0 TCTGGATTCT 0.992062 -34 GTCGGGATTCCTGTTTTTATAC 1 92 0 TCGGGATCCT 0.933605 -12 TGTGTAAACATCTGGACGGCTAAAATCCTTC 2 150 0 TCTGGACGCT 0.988014 -87 CGTCAATACATCTGGACATCTAAACTTCTTT 3 77 1 TCTGGACTCT 0.991903 -200 ATATTTGCAGTCCGGTTTGCTTTGCATACCG 4 103 1 TCCGGTTGCT 0.904521 -198 CATCTTTACATCTGGACGTCTAAACGGATAG 4 233 1 TCTGGACTCT 0.991903 -68 TGGCAAATTTTCTGGTTATCTTCAGCTATCT 5 93 1 TCTGGTTTCT 0.978611 -64 TCTTCAGCTATCTGGATGTCTAAACGTATAA 5 111 1 TCTGGATTCT 0.992062 -46 ******* *** Masking position 1 Map Score: 14.5071 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 TTTTATACGTCTGGATGTCTAAACTAGCAT 1 70 0 CTGGATGTCT 0.99403 -34 GTGTAAACATCTGGACGGCTAAAATCCTTC 2 150 0 CTGGACGGCT 0.985944 -87 ACCGCCAATTATGGATGTGTAAACATCTGG 2 166 0 ATGGATGTGT 0.863068 -71 CATTGTGTTAATGGACGTCAATACATCTGG 3 62 1 ATGGACGTCA 0.915432 -215 GTCAATACATCTGGACATCTAAACTTCTTT 3 78 1 CTGGACATCT 0.983714 -199 ATCTTTACATCTGGACGTCTAAACGGATAG 4 234 1 CTGGACGTCT 0.996228 -67 GGCAAATTTTCTGGTTATCTTCAGCTATCT 5 94 1 CTGGTTATCT 0.872198 -63 CTTCAGCTATCTGGATGTCTAAACGTATAA 5 112 1 CTGGATGTCT 0.99403 -45 ********** Masking position 2 Map Score: 13.6312 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 GACGAATCCGGCAAGAAGCAATAAGTACATGG 4 64 1 GAAGAAGCAT 0.95933 -237 CATGTTGAAGGTGAGAAAGTTTCAAGGAAAAG 5 49 0 GGAGAAAGTT 0.796689 -108 ATCGAGAGTTGGGCGAGGGATTGGCCTTTTGA 6 33 1 GGCGAGGGAT 0.945882 -268 CAGTCTCGGCGCGAAAAGCAGTGCGCCCCATT 6 98 0 GGAAAAGCAT 0.748564 -203 TCTGAGAGATGAGAGAGGCAGTGTTTTACGTA 6 169 1 GGAGAGGCAT 0.989323 -132 TCCCATGAGAGAAAGAGGCTTTTCTACGTAAA 6 193 0 GAAGAGGCTT 0.98317 -108 TCTCTCATGGGAAAGAGGCTTTTTGTTGTGAG 6 213 1 GAAGAGGCTT 0.98317 -88 ATCCGCGGGTGAAAGAGAGTGTTTTACATATA 6 265 1 GAAGAGAGTT 0.902789 -36 TTTCAAAGATGTAAGAGGGAATTGTAATGTTT 7 126 0 GAAGAGGGAT 0.983081 -175 * ******** * Masking position 6 Map Score: 7.87515 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 195 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 TATGCCAATTCTTCAGGATGCGCCCGCGAA 1 35 1 CTTCAGGATG 0.938816 -69 CGGTCACTTACTTCAGTAAGCTCCCGGGGA 2 79 0 CTTCAGTAAG 0.728405 -158 GGCTAAAATCCTTCGTCTTTTAAATTTATG 2 134 0 CTTCGTCTTT 0.890503 -103 AAGTCCTTCACTTCGGCATGAATAATTTGC 2 215 0 CTTCGGCATG 0.983026 -22 ACTTAATCCTCTTCGTCAATAAATTGAGAC 3 252 0 CTTCGTCAAT 0.843471 -25 GATGAAAAAACTTCAGGATGGTAAGAAAAA 4 141 0 CTTCAGGATG 0.938816 -160 GGTTGACGCCCTTCGGCTTTTCCTTCATCT 4 208 1 CTTCGGCTTT 0.961262 -93 TCGGCTTTTCCTTCATCTTTACATCTGGAC 4 220 1 CTTCATCTTT 0.882443 -81 ACTTTCTCACCTTCAACATGCAGGCTCGAC 5 61 1 CTTCAACATG 0.873935 -96 TTCTGGTTATCTTCAGCTATCTGGATGTCT 5 102 1 CTTCAGCTAT 0.912056 -55 ********** Masking position 3 Map Score: 9.52264 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 663 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 CTTCCCTAAATTCAAAATCCATAGGATTTACA 2 31 0 TTAAAATCAT 0.709453 -206 ATCCTTCGTCTTTTAAATTTATGGTGCGTTGG 2 125 0 TTTAAATTAT 0.881033 -112 ATTTGGGATTTGCTCAATCTATACGCAAAGAA 3 102 0 TGTCAATCAT 0.960436 -175 GTGTGGTCTGGTCTCAATTTATTGACGAAGAG 3 242 1 GTTCAATTAT 0.752132 -35 CCTAATCCTATGATAATTCAATATATTTCATT 4 15 0 TGTAATTCAT 0.848365 -286 TAAGGCACGGTGCTAATTCCATCAGATTGTGT 6 138 1 TGTAATTCAT 0.848365 -163 TTCTTATGAGTTCTTAATTGATGTTTACATTT 7 27 0 TTTTAATTAT 0.692397 -274 CGTCAGTTCATTATCAATTCATATGGCTCGTT 7 74 1 TTTCAATTAT 0.935692 -227 GTTTTTTATCTTATCATTCTATAAAACATTAC 7 103 1 TTTCATTCAT 0.939166 -198 TTCACGCCAATTTTCAATCTATCTATACGTGT 7 230 0 TTTCAATCAT 0.971506 -71 ** ****** ** Masking position 6 Map Score: 3.10041 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 115 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 TGCACCTGTCGGCGTGATAATGCATATAATTT 3 142 0 GGCGTGATTG 0.926223 -135 TTACCGTACAGGCGTTACCGTGACATCGTGTA 3 175 0 GGCGTTACTG 0.982454 -102 GACGCCCTTCGGCTTTTCCTTCATCTTTACAT 4 212 1 GGCTTTTCTC 0.938153 -89 TTCTAACGTAGTCTTTTCCTTGAAACTTTCTC 5 37 1 GTCTTTTCTG 0.910989 -120 TCAACATGCAGGCTCGACATTGGCAAATTTTC 5 73 1 GGCTCGACTG 0.937002 -84 GAGAGAAAGAGGCTTTTCTACGTAAAACACTG 6 187 0 GGCTTTTCCG 0.960541 -114 ATGGGAAAGAGGCTTTTTGTTGTGAGAAAACC 6 219 1 GGCTTTTTTG 0.954469 -82 GAAACCAAAAGGCGTGTCAGTGCGTTTTATTT 7 171 1 GGCGTGTCTG 0.988771 -130 ******** ** Masking position 3 Map Score: 4.60902 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 443 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 GCCAATTCTTCAGGATGCGCCCGCGAATATT 1 38 1 CAGGATCGCC 0.986567 -66 CGTATAAAAACAGGAATCCCGAC 1 91 1 CAGGAACCCG 0.803196 -13 TCACTTACTTCAGTAAGCTCCCGGGGATGAA 2 75 0 CAGTAACTCC 0.938221 -162 GAGGAATATACAGTAACCGCCAATTATGGAT 2 180 0 CAGTAACGCC 0.987539 -57 TGGGTACTGACCGTAAACCCGCATAGTTTAC 3 203 0 CCGTAACCCG 0.963092 -74 TTGCTTCTTGCCGGATTCGTCGTAAACGCTT 4 54 0 CCGGATCGTC 0.886964 -247 TCTTAGCAGCCTGTATCCGCGGGTGAAAGAG 6 251 1 CTGTATCGCG 0.933704 -50 ****** **** Masking position 5 Map Score: 2.08576 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 666 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 TTTACATATAATTAGAGGAAGAAAAA 2 7 0 ATTAGAGGAA 0.92614 -230 AATGACTAAAAGGAGAGAAA 5 1 0 AGGAGAGAAA 0.965815 -156 TGCATGTTGAAGGTGAGAAAGTTTCAAGGA 5 53 0 AGGTGAGAAA 0.854342 -104 CCAACTCTCGATAAGAGAAAATGTTATTAA 6 15 0 ATAAGAGAAA 0.949069 -286 CCTCTTTCCCATGAGAGAAAGAGGCTTTTC 6 201 0 ATGAGAGAAA 0.976736 -100 TTATAGAATGATAAGATAAAAAACGAGCCA 7 97 0 ATAAGATAAA 0.707348 -204 AATTTTCTTCATTATAGGAATTTTCACGCC 7 254 0 ATTATAGGAA 0.619256 -47 ********** Masking position 6 Map Score: 1.40176 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 95 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 10 GCATGAATATTCGCGGGCGCATCCTGAAGA 1 44 0 TCGCGGGCGC 0.966244 -60 GTTTATTCATCCCCGGGAGCTTACTGAAGT 2 70 1 CCCCGGGAGC 0.991355 -167 CGTTTCTCCACCCCGGTCACTTACTTCAGT 2 92 0 CCCCGGTCAC 0.985136 -145 ACCGACAAAGCCCAGGGAACTTCATCAC 3 9 0 CCCAGGGAAC 0.955358 -268 TTACACGATGTCACGGTAACGCCTGTACGG 3 174 1 TCACGGTAAC 0.839269 -103 TCTCTTTCACCCGCGGATACAGGCTGCTAA 6 253 0 CCGCGGATAC 0.904399 -48 ********** Masking position 5 Map Score: 0.289062 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 261 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 ********** No masking Map Score: -1.18417e-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: -1.18417e-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: -1.18417e-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