AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imetJ_ecoli_hinf_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 HI0122 274 cystathionine beta-lyase (metC) #7 HI0294 246 met repressor (metJ) #8 HI1444 300 5,10 methylenetetrahydrofolate reductase (metF) #9 HI1702 192 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (metE) #10 HI1739 300 transcriptional activator (metR) Motif number 1 TATACGTCTGGATGTCTAAACTAGCATGAAT 1 66 0 GATGCTAAAC 0.98995 -38 TAGACATCCAGACGTATAAAAACAGGAATCC 1 79 1 GACGATAAAA 0.937709 -25 AGCTCCCGGGGATGAATAAACTTGCCGCCTT 2 60 0 GATGATAAAC 0.972132 -177 TAAACATCTGGACGGCTAAAATCCTTCGTCT 2 146 0 GACGCTAAAA 0.977016 -91 GCCAATTATGGATGTGTAAACATCTGGACGG 2 162 0 GATGGTAAAC 0.927299 -75 TGTGTTAATGGACGTCAATACATCTGGACAT 3 65 1 GACGCAATAC 0.754651 -212 AATACATCTGGACATCTAAACTTCTTTGCGT 3 81 1 GACACTAAAC 0.967708 -196 AATCAGGGAAGATGAAAAAACTTCAGGATGG 4 150 0 GATGAAAAAC 0.858242 -151 TTTACATCTGGACGTCTAAACGGATAGATGT 4 237 1 GACGCTAAAC 0.994477 -64 CAGCTATCTGGATGTCTAAACGTATAAGCGT 5 115 1 GATGCTAAAC 0.98995 -42 AAATAATTCTGACGTCTACACAGAATCCCTA 6 135 0 GACGCTACAC 0.963326 -140 TAACAATCTAGACGGCTAAACTTCCAAAATA 7 160 0 GACGCTAAAC 0.994477 -87 ATCGTTATTTGATAGATAAAAGAATGCTTGA 9 42 1 GATAATAAAA 0.578152 -151 TAATCATTTAGACGGCTAAACGTCTATACCA 9 145 0 GACGCTAAAC 0.994477 -48 ATCTATCTAAGATAGATAAAATTAAATTAAG 10 97 1 GATAATAAAA 0.578152 -204 **** ****** Masking position 8 Map Score: 29.944 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 177 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 TCGCGGGCGCATCCTGAAGAATTGGCATAAAG 1 32 0 ATCCGAAGAT 0.872521 -72 TAGTTTAGACATCCAGACGTATAAAAACAGGA 1 74 1 ATCCGACGAT 0.975484 -30 ATGTGTAAACATCTGGACGGCTAAAATCCTTC 2 150 0 ATCTGACGCT 0.995917 -87 ACGTCAATACATCTGGACATCTAAACTTCTTT 3 76 1 ATCTGACACT 0.95105 -201 AATGCATATAATTTTAACGGCTATTTGGGATT 3 124 0 ATTTAACGCT 0.827959 -153 TTTTCTTACCATCCTGAAGTTTTTTCATCTTC 4 142 1 ATCCGAAGTT 0.796257 -159 TCATCTTTACATCTGGACGTCTAAACGGATAG 4 232 1 ATCTGACGCT 0.99596 -69 ATCTTCAGCTATCTGGATGTCTAAACGTATAA 5 110 1 ATCTGATGCT 0.960276 -47 ACAACAAATAATTCTGACGTCTACACAGAATC 6 139 0 ATTCGACGCT 0.982793 -136 ATAAATAACAATCTAGACGGCTAAACTTCCAA 7 164 0 ATCTGACGCT 0.995957 -83 TTTTTTAATCATTTAGACGGCTAAACGTCTAT 9 149 0 ATTTGACGCT 0.983888 -44 **** **** ** Masking position 7 Map Score: 17.0895 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 281 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 TAAGAAAAAGAAAATCCGGTATGCAAAGCA 4 120 0 AAAATCCGGT 0.967411 -181 ATCTTTAGCTAAAGTGCGGTCAATTTTTCT 6 11 0 AAAGTGCGGT 0.994262 -264 CAGATGAAGTAAAATCAGGTGCGGATAGGA 6 203 1 AAAATCAGGT 0.821187 -72 GTTCTTAAAAAAAGTGCGATGATTTTTATA 7 129 0 AAAGTGCGAT 0.950864 -118 AACGAAAAAGAAAGTGCGGTAATTTTTTGT 8 78 0 AAAGTGCGGT 0.994262 -223 TTTTCGTTGTAAAATGGGGTAAATCATTGC 8 100 1 AAAATGGGGT 0.972532 -201 ATTGCTAACAAAAGTGCGGTAGTTTTGAGT 8 125 1 AAAGTGCGGT 0.994262 -176 CCCAGTCCTTAAACTGGGGTTCTATATTTA 10 165 0 AAACTGGGGT 0.954061 -136 ********** Masking position 3 Map Score: 12.2179 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 48 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 GCTATTTGGGATTTGCTCAATCTATACGCAA 3 106 0 ATTTCTCAAT 0.874053 -171 TGCATACCGGATTTTCTTTTTCTTACCATCC 4 125 1 ATTTCTTTTT 0.590511 -176 ACGAGCTTTAATTTTATCAATTATTTATAAA 6 92 0 ATTTATCAAT 0.814585 -183 CGTCAGAATTATTTGTTGTTTTCTCTTTATT 6 152 1 ATTTTTGTTT 0.578789 -123 TTTTCTCTTTATTTTTTCCATTGCCTAATAC 6 170 1 ATTTTTCCAT 0.735686 -105 ATATTTCCTTATTTAAATTAACT 6 262 0 ATTTCTTATT 0.7833 -13 TAATTCCAACATTTATTCATT 7 1 0 ATTTTTCATT 0.927936 -246 AAGTGCGATGATTTTTATATTAAATGCTAAT 7 117 0 ATTTTATATT 0.556307 -130 CTAGATTGTTATTTATTTGATTTTTAATTAG 7 180 1 ATTTTTTGAT 0.682277 -67 AATACAATAGATTTGTTTTTTAGCGCAAAAA 8 13 0 ATTTTTTTTT 0.798584 -288 AATCTATTGTATTTATTTAACACGCATTTAT 8 31 1 ATTTTTTAAC 0.596804 -270 ATAATTATCCATTTATTGAATTATTAATAAT 8 189 1 ATTTTTGAAT 0.834824 -112 GTCAATTTCAATTTATTCATTAAAAGTATGA 8 222 0 ATTTTTCATT 0.927936 -79 CTAAAATAGTATTTGTACAATAAAATAGGTT 8 262 0 ATTTTACAAT 0.706491 -39 TTGATTATGAATTTATTTAATGTAAATCCTG 9 69 1 ATTTTTTAAT 0.934936 -124 ATTTAAAGTAATTTTTTTAATCATTTAGACG 9 162 0 ATTTTTTAAT 0.93621 -31 ACTTAATTTAATTTTATCTATCTTAGATAGA 10 98 0 ATTTATCTAT 0.637776 -203 TCTTTATCTAATTTGTTTAATTCTGTTTTTA 10 133 0 ATTTTTTAAT 0.93637 -168 GGGGTTCTATATTTATTCTTTATCTAATTTG 10 149 0 ATTTTTCTTT 0.837101 -152 TAAATAATTAATTTTATTAATTAGCATATTT 10 223 1 ATTTATTAAT 0.772343 -78 **** ****** Masking position 4 Map Score: 15.5793 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 328 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 5 GTAAATCCTATGGATTTTGAATTTAGGGAAGG 2 32 1 TGATTTGAAT 0.928941 -205 TTTAATTTTATCAATTATTTATAAAAAGCGAC 6 85 0 TAATTTTTAT 0.621632 -190 ATTCGAATAATCAATTCTTATTAATTCCAACA 7 21 0 TAATTTTATT 0.815408 -226 TTTAGCCGTCTAGATTGTTATTTATTTGATTT 7 171 1 TGATTTTATT 0.938904 -76 TGTTATTTATTTGATTTTTAATTAGAATACGG 7 186 1 TGATTTTAAT 0.946817 -61 ATTCAATAAATGGATAATTATTGTTCAATAAT 8 178 0 TGATATTATT 0.831472 -123 ATCCATTTATTGAATTATTAATAATAATCATA 8 195 1 TAATTTTAAT 0.836532 -106 AAAAGAATGCTTGATTATGAATTTATTTAATG 9 59 1 TGATTTGAAT 0.928941 -134 GATTTATATTTAGATTTTTTATTTGATAACCT 10 68 0 TGATTTTTAT 0.851094 -233 CTATCTTAGATAGATTTATATTTAGATTTTTT 10 80 0 TGATTATATT 0.758381 -221 TCTAATTTGTTTAATTCTGTTTTTACTTAACT 10 126 0 TAATTTGTTT 0.510132 -175 TTAAACAAATTAGATAAAGAATAAATATAGAA 10 144 1 TGATAAGAAT 0.461558 -157 ATTAATTATTTAGATAATTATTTTAGTTAAAA 10 203 0 TGATATTATT 0.831472 -98 * **** ***** Masking position 4 Map Score: 6.76721 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 115 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 TATGCCAATTCTTCAGGATGCGCCCGCGAA 1 35 1 CTTCAGGATG 0.820162 -69 GGCTAAAATCCTTCGTCTTTTAAATTTATG 2 134 0 CTTCGTCTTT 0.915265 -103 AAGTCCTTCACTTCGGCATGAATAATTTGC 2 215 0 CTTCGGCATG 0.970216 -22 ACTTAATCCTCTTCGTCAATAAATTGAGAC 3 252 0 CTTCGTCAAT 0.881003 -25 GATGAAAAAACTTCAGGATGGTAAGAAAAA 4 141 0 CTTCAGGATG 0.820162 -160 GGTTGACGCCCTTCGGCTTTTCCTTCATCT 4 208 1 CTTCGGCTTT 0.953584 -93 TCGGCTTTTCCTTCATCTTTACATCTGGAC 4 220 1 CTTCATCTTT 0.870944 -81 ACCTTACCTCATCAATCGCTTGTAGT 4 285 0 CCTCATCAAT 0.491024 -16 ACTTTCTCACCTTCAACATGCAGGCTCGAC 5 61 1 CTTCAACATG 0.725211 -96 TTCTGGTTATCTTCAGCTATCTGGATGTCT 5 102 1 CTTCAGCTAT 0.820257 -55 TGAATTGATTCATCGTTATTTGATAGATAA 9 31 1 CATCGTTATT 0.311036 -162 CCCACACTACCATCGGCATTACAGCGTT 10 9 0 CATCGGCATT 0.907648 -292 ********** Masking position 3 Map Score: 4.88568 Number of sites scoring better than the average of aligned sites = 1348 Number in coding regions = 1247 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 7 CGCTTGAGGAATATACAGTAACCGCCAATTATG 2 183 0 ATATAATAAC 0.89233 -54 CGGACTGCAAATATAAACTAACCATGTACTTAT 4 84 0 ATATAATAAC 0.89233 -217 ATCAGAGATAATTTAGAATAAACCATCTTTAGC 6 32 0 ATTTAATAAC 0.944277 -243 TTTATCAATTATTTATAAAAAGCGACCTTAGGT 6 78 0 ATTTAAAAAC 0.852986 -197 AATGGAAAAAATAAAGAGAAAACAACAAATAAT 6 159 0 ATAAAAAAAC 0.503474 -116 ATATTTCCTTATTTAAATTAACTTATAGGGCAA 6 252 0 ATTTAATAAT 0.933292 -23 GTGCGATGATTTTTATATTAAATGCTAATAAAA 7 113 0 TTTTAATAAT 0.608354 -134 TTATTGAATTATTAATAATAATCATACTTTTAA 8 201 1 ATTAAATAAC 0.892288 -100 TATTTTCAGGATTTACATTAAATAAATTCATAA 9 73 0 ATTTAATAAT 0.749593 -120 AATAACTCCAATTTAAAGTAATTTTTTTAATCA 9 170 0 ATTTAATAAT 0.861914 -23 AGATAGATAAAATTAAATTAAGTTAAGTAAAAA 10 106 1 AATTAATAAT 0.818975 -195 GTAAAAACAGAATTAAACAAATTAGATAAAGAA 10 132 1 AATTAAAAAT 0.581553 -169 AACAAATTAGATAAAGAATAAATATAGAACCCC 10 147 1 ATAAAATAAT 0.740193 -154 TATGCTAATTAATAAAATTAATTATTTAGATAA 10 218 0 AATAAATAAT 0.664716 -83 ***** * *** * Masking position 7 Map Score: 8.92507 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 60 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 GGTAACGCCTGTACGGTAAACTATGCGGGTT 3 188 1 GTACGGTAAC 0.923236 -89 AGCGTATGTAGTGAGGTAATCAGGTT 5 141 1 GTGAGGTATC 0.965091 -16 TTTAGCTAAAGTGCGGTCAATTTTTCT 6 7 0 GTGCGGTAAT 0.973339 -268 CTTAAAAAAAGTGCGATGATTTTTATATTAA 7 125 0 GTGCGATATT 0.915864 -122 CGGACAATTTGTAAGGTTATCAATAAGCACT 7 215 1 GTAAGGTATC 0.882928 -32 GAAAAAGAAAGTGCGGTAATTTTTTGTGTAT 8 74 0 GTGCGGTATT 0.988225 -227 GCTAACAAAAGTGCGGTAGTTTTGAGTATGT 8 128 1 GTGCGGTGTT 0.962718 -173 ******* *** Masking position 7 Map Score: 4.12671 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 229 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 CTTCCTCTAATTATATGTAAATCCTATGGAT 2 16 1 TTATATTAAA 0.534465 -221 TTCTAATGAAATATATTGAAT 4 1 1 TTCTAAGAAA 0.911088 -300 GGTGAGAAAGTTTCAAGGAAAAGACTACGTT 5 41 0 TTTCAAGAAA 0.826391 -116 AGGTCGCTTTTTATAAATAATTGATAAAATT 6 83 1 TTATAATAAT 0.534473 -192 ATTGTCCGTATTCTAATTAAAAATCAAATAA 7 192 0 TTCTAATAAA 0.81668 -55 TTTTGTGTATTTTTATAGAAAGATAAATGCG 8 53 0 TTTTATGAAA 0.80695 -248 TTACCCCATTTTACAACGAAAAAGAAAGTGC 8 91 0 TTACAAGAAA 0.804908 -210 ATAATCATACTTTTAATGAATAAATTGAAAT 8 218 1 TTTTAAGAAT 0.810499 -83 TTTTAAGGAAATAAGTTAGCT 9 1 1 TTTTAAGAAA 0.937886 -192 GGGTTTTGTATTTTAACTAAAATAATTATCT 10 193 1 TTTTAATAAA 0.868737 -108 ****** **** Masking position 5 Map Score: 2.24567 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 83 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 10 ATTTCACCGACAAAGCCCAGGGAACTTCAT 3 14 0 CAAAGCCCAG 0.936084 -263 TTCAAAGGGTGCAAGCCCACCATTCGAATA 7 44 0 GCAAGCCCAC 0.923906 -203 AATTACCACTAAAACCCTACGCTGTCTAGC 7 83 1 AAAACCCTAC 0.880811 -164 CTCACATGGGGAAACCCCACACTACCATCG 10 24 0 GAAACCCCAC 0.980977 -277 GAATAAATATAGAACCCCAGTTTAAGGACT 10 162 1 AGAACCCCAG 0.955594 -139 GTTAAAATACAAAACCCCAGTCCTTAAACT 10 180 0 AAAACCCCAG 0.979495 -121 ********** Masking position 4 Map Score: 0.303066 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 106 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 CCAATTCTTCAGGATGCGCCCGCGAATATTCATG 1 39 1 AGGAGCCGCG 0.991107 -65 CACTTACTTCAGTAAGCTCCCGGGGATGAATAAA 2 71 0 AGTAGCCGGG 0.992241 -166 AGCTTACTGAAGTAAGTGACCGGGGTGGAGAAAC 2 87 1 AGTAGCCGGG 0.992241 -150 GTGATGAAGTTCCCTGGGCTTTGTCGG 3 4 1 ATGAGCCTGG 0.841269 -273 GAATTATCATAGGATTAGGCCGGATTAAGCGTTT 4 28 1 AGGATCCGGA 0.86781 -273 TTAAGCGTTTACGACGAATCCGGCAAGAAGCAAT 4 52 1 ACGAGCCGGC 0.969375 -249 CCCATGTGAGAGTAGGGCACCGCCAGGTTATCAA 10 44 1 AGTAGCCGCC 0.965759 -257 **** * ***** Masking position 4 Map Score: 0.871168 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 135 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ATGAAATATATTGAATTATCATAGGATTAGGC 4 16 1 TTGATTACAT 0.725486 -285 TGCAGTCCGGTTTGCTTTGCATACCGGATTTT 4 108 1 TTTCTTTCAT 0.73879 -193 CGGATTTTCTTTTTCTTACCATCCTGAAGTTT 4 132 1 TTTCTTACAT 0.960659 -169 CATCCTGAAGTTTTTTCATCTTCCCTGATTTT 4 151 1 TTTTTCACTT 0.569677 -150 TTCCCTGATTTTTCCTCACCATCATTGGTCAT 4 171 1 TTTCTCACAT 0.903585 -130 CTTAGGTGGCTTTTTTTATCATCAGAGATAAT 6 53 0 TTTTTTACAT 0.939004 -222 GCTGTCTAGCTTTTATTAGCATTTAATATAAA 7 103 1 TTTATTACAT 0.939005 -144 TTATTTGATTTTTAATTAGAATACGGACAATT 7 192 1 TTTATTAAAT 0.524853 -55 ATCTATTGTATTTATTTAACACGCATTTATCT 8 32 1 TTTTTTACAC 0.725488 -269 TTAAAGTAATTTTTTTAATCATTTAGACGGCT 9 159 0 TTTTTAACAT 0.684106 -34 TAATTCTGTTTTTACTTAACTTAATTTAATTT 10 115 0 TTTCTTACTT 0.845467 -186 AATTAATTTTATTAATTAGCATATTTCTAATT 10 228 1 ATTATTACAT 0.640688 -73 *** **** *** Masking position 6 Map Score: 2.40276 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 174 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 13 CGAATATTCATGCTAGTTTAGACATCCAGAC 1 61 1 TCTAGTTTAG 0.760255 -43 GCTCGTTAGCATCTATTTTAGGGATTCTGTG 6 117 1 ACTATTTTAG 0.970249 -158 TTGAAACCATAGTTATTTTTGCCCTATAAGT 6 234 1 ATTATTTTTG 0.72577 -41 TTTTTTAAGAACTTATTTTGGAAGTTTAGCC 7 147 1 ATTATTTTGG 0.796853 -100 TCATATTAAAACCTATTTTATTGTACAAATA 8 253 1 ACTATTTTAT 0.784569 -48 ATTGTACAAATACTATTTTAGAATCCTAAAG 8 272 1 TCTATTTTAG 0.922715 -29 ATTTAATTTTATCTATCTTAGATAGATTTAT 10 93 0 ACTATCTTAG 0.896504 -208 TTATTTAGATAATTATTTTAGTTAAAATACA 10 199 0 ATTATTTTAG 0.927262 -102 * ********* Masking position 5 Map Score: 0.33343 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 35 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 ********** No masking Map Score: -3.21633e-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 15 ATAAAAACAGGAATCCCGAC 1 94 1 GAATCCCGAC 0.976016 -10 GTACTGACCGTAAACCCGCATAGTTTACCG 3 201 0 TAAACCCGCA 0.845391 -76 CGTAAACGCTTAATCCGGCCTAATCCTATG 4 35 0 TAATCCGGCC 0.942967 -266 CGTTTACGACGAATCCGGCAAGAAGCAATA 4 57 1 GAATCCGGCA 0.955612 -244 GTATGCAAAGCAAACCGGACTGCAAATATA 4 102 0 CAAACCGGAC 0.798043 -199 CGTCTACACAGAATCCCTAAAATAGATGCT 6 124 0 GAATCCCTAA 0.698161 -151 TTCCATTGCCTAATACCGCAGATGAAGTAA 6 185 1 TAATACCGCA 0.672408 -90 TTTTTAATTAGAATACGGACAATTTGTAAG 7 200 1 GAATACGGAC 0.866121 -47 CTCACATGGGGAAACCCCACACTACCATCG 10 24 0 GAAACCCCAC 0.779402 -277 ********** Masking position 3 Map Score: 0.472337 Number of sites scoring better than the average of aligned sites = 1158 Number in coding regions = 1069 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069