AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imetJ_ecoli_hinf_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 #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 HI1704 107 conserved hypothetical protein #11 HI1739 300 transcriptional activator (metR) Motif number 1 TATACGTCTGGATGTCTAAACTAGCATGAAT 1 66 0 GATGCTAAAC 0.98779 -38 TAGACATCCAGACGTATAAAAACAGGAATCC 1 79 1 GACGATAAAA 0.925171 -25 AGCTCCCGGGGATGAATAAACTTGCCGCCTT 2 60 0 GATGATAAAC 0.966274 -177 TAAACATCTGGACGGCTAAAATCCTTCGTCT 2 146 0 GACGCTAAAA 0.972155 -91 GCCAATTATGGATGTGTAAACATCTGGACGG 2 162 0 GATGGTAAAC 0.912861 -75 TGTGTTAATGGACGTCAATACATCTGGACAT 3 65 1 GACGCAATAC 0.716409 -212 AATACATCTGGACATCTAAACTTCTTTGCGT 3 81 1 GACACTAAAC 0.960957 -196 AATCAGGGAAGATGAAAAAACTTCAGGATGG 4 150 0 GATGAAAAAC 0.832565 -151 TTTACATCTGGACGTCTAAACGGATAGATGT 4 237 1 GACGCTAAAC 0.993284 -64 CAGCTATCTGGATGTCTAAACGTATAAGCGT 5 115 1 GATGCTAAAC 0.98779 -42 AAATAATTCTGACGTCTACACAGAATCCCTA 6 135 0 GACGCTACAC 0.9557 -140 TAACAATCTAGACGGCTAAACTTCCAAAATA 7 160 0 GACGCTAAAC 0.993284 -87 ATCGTTATTTGATAGATAAAAGAATGCTTGA 9 42 1 GATAATAAAA 0.52955 -151 TAATCATTTAGACGGCTAAACGTCTATACCA 9 145 0 GACGCTAAAC 0.993284 -48 ATCTATCTAAGATAGATAAAATTAAATTAAG 11 97 1 GATAATAAAA 0.52955 -204 **** ****** Masking position 8 Map Score: 29.3172 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 TAGTTTAGACATCCAGACGTATAAAAACAGGA 1 74 1 ATCCGACGAT 0.934684 -30 ATGTGTAAACATCTGGACGGCTAAAATCCTTC 2 150 0 ATCTGACGCT 0.996628 -87 ACGTCAATACATCTGGACATCTAAACTTCTTT 3 76 1 ATCTGACACT 0.966985 -201 AATGCATATAATTTTAACGGCTATTTGGGATT 3 124 0 ATTTAACGCT 0.905658 -153 TCATCTTTACATCTGGACGTCTAAACGGATAG 4 232 1 ATCTGACGCT 0.996663 -69 ATCTTCAGCTATCTGGATGTCTAAACGTATAA 5 110 1 ATCTGATGCT 0.966986 -47 ACAACAAATAATTCTGACGTCTACACAGAATC 6 139 0 ATTCGACGCT 0.979535 -136 ATAAATAACAATCTAGACGGCTAAACTTCCAA 7 164 0 ATCTGACGCT 0.996661 -83 TTTTTTAATCATTTAGACGGCTAAACGTCTAT 9 149 0 ATTTGACGCT 0.989888 -44 **** **** ** Masking position 7 Map Score: 16.4083 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 54 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 TAAGAAAAAGAAAATCCGGTATGCAAAGCA 4 120 0 AAAATCCGGT 0.962966 -181 ATCTTTAGCTAAAGTGCGGTCAATTTTTCT 6 11 0 AAAGTGCGGT 0.993455 -264 CAGATGAAGTAAAATCAGGTGCGGATAGGA 6 203 1 AAAATCAGGT 0.8009 -72 GTTCTTAAAAAAAGTGCGATGATTTTTATA 7 129 0 AAAGTGCGAT 0.944292 -118 AACGAAAAAGAAAGTGCGGTAATTTTTTGT 8 78 0 AAAGTGCGGT 0.993455 -223 TTTTCGTTGTAAAATGGGGTAAATCATTGC 8 100 1 AAAATGGGGT 0.968762 -201 ATTGCTAACAAAAGTGCGGTAGTTTTGAGT 8 125 1 AAAGTGCGGT 0.993455 -176 CCCAGTCCTTAAACTGGGGTTCTATATTTA 11 165 0 AAACTGGGGT 0.947893 -136 ********** Masking position 3 Map Score: 11.8818 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 TATATTCCTCAAGCGCAAATTATTCATGCCGAAGTGA 2 201 1 AAAATATTAT 0.913276 -36 CACAACATATAACTACAAGCGATTGATGAGGTAAGGT 4 274 1 AAAACATTAT 0.724489 -27 TAACGAGCTTTAATTTTATCAATTATTTATAAAAAGC 6 88 0 TATACATTTT 0.59457 -187 ATAAAGAGAAAACAACAAATAATTCTGACGTCTACAC 6 145 0 AAAATATTTG 0.810578 -130 ATAGGAATTGAAACCATAGTTATTTTTGCCCTATAAG 6 227 1 AATATATTTT 0.881884 -48 TGTTGGAATTAATAAGAATTGATTATTCGAATGGTGG 7 21 1 AAAATATTTT 0.955277 -226 ATTATTGTTCAATAATAACTAATTTTTAGATCAACAC 8 157 0 AAAATATTTT 0.521191 -144 TAATTCAATAAATGGATAATTATTGTTCAATAATAAC 8 175 0 AATATATTTT 0.881884 -126 AATATGAGTCAATTTCAATTTATTCATTAAAAGTATG 8 223 0 AAAATATTAT 0.913263 -78 GGAAATAAGTTAGCTGAATTGATTCATCGTTATTTGA 9 17 1 TAAATATTAT 0.892113 -176 CTTCATTTATTATGCAAACTTATTATTTTCAGGATTT 9 92 0 TAAATATTTT 0.959373 -101 AATAACTCCAATTTAAAGTAATTTTTTTAATCATTT 9 167 0 AAAATATTTT 0.9676 -26 ATCGGTCGCATATGATAACTTATTTTCGCTGAATTAA 10 32 0 TAAATATTTC 0.863382 -76 TGTTTTTACTTAACTTAATTTAATTTTATCTATCTTA 11 104 0 TAAATAATTT 0.668203 -197 TTTTGTATTTTAACTAAAATAATTATCTAAATAATTA 11 196 1 TAAATATTTC 0.863764 -105 ATATGCTAATTAATAAAATTAATTATTTAGATAATTA 11 215 0 TAAATATTTT 0.959318 -86 ** ** * *** ** Masking position 8 Map Score: 12.6487 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 44 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 TGCAAATATAAACTAACCATGTACTTATTGCTTCTTG 4 75 0 AATACAATTA 0.93575 -226 GCAATGGAAAAAATAAAGAGAAAACAACAAATAATTC 6 157 0 AATAAAACAA 0.91364 -118 ATTAAAAATCAAATAAATAACAATCTAGACGGCTAAA 7 171 0 AATAAAACTA 0.93575 -76 CTTTCTATAAAAATACACAAAAAATTACCGCACTTTC 8 62 1 AATAAAATTA 0.952002 -239 ATTGAACAATAATTATCCATTTATTGAATTATTAATA 8 181 1 AATACAATGA 0.794591 -120 TTTATCTATCAAATAACGATGAATCAATTCAGCTAAC 9 25 0 AATACAACAA 0.885955 -168 ATTTTCGCTGAATTAAACAGAAATTTAAGGACAACAA 10 11 0 AATAAAATTA 0.952002 -97 TTAGATTTAGAAAAACAAACGAAATAAG 10 90 1 AAAAAAATAA 0.605245 -18 TAAAAAATCTAAATATAAATCTATCTAAGATAGATAA 11 79 1 AATAAAACTA 0.93575 -222 AAATTAAGTTAAGTAAAAACAGAATTAAACAAATTAG 11 120 1 AATAAAATTA 0.952002 -181 GAATTAAACAAATTAGATAAAGAATAAATATAGAACC 11 141 1 AATAAAATAA 0.935097 -160 TAACTAAAATAATTATCTAAATAATTAATTTTATTAA 11 206 1 AATACAATTA 0.93575 -95 AATACATTAAAATTAGAAATATGCTAATTAATAAAAT 11 233 0 AATAAAGTAA 0.694415 -68 ** ** * * * *** Masking position 9 Map Score: 9.52419 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 28 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 TTCGCGGGCGCATCCTGAAGAATTGGCATA 1 35 0 CATCCTGAAG 0.897 -69 CATAAATTTAAAAGACGAAGGATTTTAGCC 2 134 1 AAAGACGAAG 0.92 -103 GCAAATTATTCATGCCGAAGTGAAGGACTT 2 215 1 CATGCCGAAG 0.982338 -22 GTCTCAATTTATTGACGAAGAGGATTAAGT 3 252 1 ATTGACGAAG 0.823926 -25 TTTTTCTTACCATCCTGAAGTTTTTTCATC 4 141 1 CATCCTGAAG 0.897 -160 AGATGAAGGAAAAGCCGAAGGGCGTCAACC 4 208 0 AAAGCCGAAG 0.972291 -93 GTCCAGATGTAAAGATGAAGGAAAAGCCGA 4 220 0 AAAGATGAAG 0.878216 -81 GTCGAGCCTGCATGTTGAAGGTGAGAAAGT 5 61 0 CATGTTGAAG 0.818962 -96 AGACATCCAGATAGCTGAAGATAACCAGAA 5 102 0 ATAGCTGAAG 0.85948 -55 AACGCTGTAATGCCGATGGTAGTGTGGG 11 9 1 AATGCCGATG 0.878469 -292 ********** Masking position 8 Map Score: 6.91996 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 760 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 7 GCCATTTGCGAAAATTTTCTGCTTTATG 1 7 1 TGCGAATTTT 0.974166 -97 TTAGCTAAAGTGCGGTCAATTTTTCT 6 5 0 TGCGGAATTT 0.983556 -270 TTAAAAAAAGTGCGATGATTTTTATATTAAAT 7 123 0 TGCGAATTTT 0.974166 -124 TTAATTAGAATACGGACAATTTGTAAGGTTAT 7 203 1 TACGGAATTT 0.885819 -44 AAAAAGAAAGTGCGGTAATTTTTTGTGTATTT 8 72 0 TGCGGATTTT 0.987323 -229 CTAACAAAAGTGCGGTAGTTTTGAGTATGTGT 8 129 1 TGCGGGTTTT 0.981276 -172 AGTTATCATATGCGACCGATTTTATCCAGTTT 10 49 1 TGCGAGATTT 0.951188 -59 ***** ***** Masking position 10 Map Score: 6.41884 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 133 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 TCAAGCGCAAATTATTCATGCCGAAGTGAAGGAC 2 209 1 ATTATTATCA 0.59721 -28 ATAATTCAATATATTTCATTAGAA 4 1 0 ATATTTATAA 0.803669 -300 ATCTTCCCTGATTTTTCCTCACCATCATTGGTCA 4 168 1 ATTTTTCTAA 0.772397 -133 CTTAGGTGGCTTTTTTTATCATCAGAGATAATTT 6 51 0 TTTTTTATAA 0.877376 -224 AATTTTATCAATTATTTATAAAAAGCGACCTTAG 6 80 0 ATTATTATAA 0.921184 -195 TATTTATTTGATTTTTAATTAGAATACGGACAAT 7 189 1 ATTTTTATAA 0.921207 -58 TAATAACTAATTTTTAGATCAACACATACTCAAA 8 148 0 TTTTTAATAA 0.770343 -153 TAAATGGATAATTATTGTTCAATAATAACTAATT 8 170 0 ATTATTTTAA 0.686906 -131 CATTTATTGAATTATTAATAATAATCATACTTTT 8 198 1 ATTATTATAA 0.921205 -103 TCAATTTCAATTTATTCATTAAAAGTATGATTAT 8 218 0 TTTATTATAA 0.877383 -83 TTCAGCTAACTTATTTCCTTAAAA 9 1 0 TTATTTCTAA 0.421015 -192 ATAAGTTTGCATAATAAATGAAGATCAAGCATTC 9 106 1 ATAATAATAA 0.657751 -87 ATATTTAGATTTTTTATTTGATAACCTGGCGGTG 11 61 0 TTTTTATTAA 0.378656 -240 AATAATTAATTTTATTAATTAGCATATTTCTAAT 11 225 1 TTTATTATAA 0.877383 -76 GGGAACCAGTATAATACATTAAAATTAGAAATAT 11 248 0 ATAATAATAA 0.657751 -53 CTAATTCTTAATTTTATATGAATATTATTA 11 281 1 ATTTTAATAA 0.845876 -20 ****** ** * * Masking position 9 Map Score: 5.25289 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 191 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 9 ACCCGCATAGTTTACCGTACAGGCGTTACC 3 188 0 TTTACCGTAC 0.926666 -89 CTTCCCTGATTTTTCCTCACCATCATTGGT 4 170 1 TTTTCCTCAC 0.871944 -131 AACCTGATTACCTCACTACATACGCT 5 141 0 ATTACCTCAC 0.965034 -16 AGAAAAATTGACCGCACTTTAGCTAAA 6 8 1 TTGACCGCAC 0.967601 -267 TACACAAAAAATTACCGCACTTTCTTTTTC 8 75 1 ATTACCGCAC 0.987905 -226 CATACTCAAAACTACCGCACTTTTGTTAGC 8 128 0 ACTACCGCAC 0.967602 -173 ********** Masking position 9 Map Score: 3.16541 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 147 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 CCTGACATTTCACCGACAAAGCCCAGGGAACTTCA 3 15 0 CAGAAGCCCA 0.980624 -262 GTGCCATTCAAAGGGTGCAAGCCCACCATTCGAAT 7 45 0 AAGAAGCCCA 0.960791 -202 TAAAAATACACAAAAAATTACCGCACTTTCTTTTT 8 69 1 CAATACCGCA 0.829258 -232 CTTTTGTTAGCAATGATTTACCCCATTTTACAACG 8 104 0 CAGTACCCCA 0.981195 -197 CCTACTCTCACATGGGGAAACCCCACACTACCATC 11 25 0 CAGAACCCCA 0.991732 -276 GATAAAGAATAAATATAGAACCCCAGTTTAAGGAC 11 156 1 AAAAACCCCA 0.965657 -145 ATTTTAGTTAAAATACAAAACCCCAGTCCTTAAAC 11 181 0 AAAAACCCCA 0.965657 -120 ** * ******* Masking position 10 Map Score: 1.77702 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 52 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 GCTATTTGGGATTTGCTCAATCTATACGCAA 3 106 0 ATTTCTCAAT 0.868457 -171 ACGAGCTTTAATTTTATCAATTATTTATAAA 6 92 0 ATTTATCAAT 0.808373 -183 TTTTCTCTTTATTTTTTCCATTGCCTAATAC 6 170 1 ATTTTTCCAT 0.752992 -105 ATATTTCCTTATTTAAATTAACT 6 262 0 ATTTCTTATT 0.674295 -13 TAATTCCAACATTTATTCATT 7 1 0 ATTTTTCATT 0.888395 -246 AAGTGCGATGATTTTTATATTAAATGCTAAT 7 117 0 ATTTTATATT 0.532112 -130 CTAGATTGTTATTTATTTGATTTTTAATTAG 7 180 1 ATTTTTTGAT 0.714932 -67 AATCTATTGTATTTATTTAACACGCATTTAT 8 31 1 ATTTTTTAAC 0.699943 -270 ATAATTATCCATTTATTGAATTATTAATAAT 8 189 1 ATTTTTGAAT 0.798593 -112 GTCAATTTCAATTTATTCATTAAAAGTATGA 8 222 0 ATTTTTCATT 0.888395 -79 CTAAAATAGTATTTGTACAATAAAATAGGTT 8 262 0 ATTTTACAAT 0.783831 -39 TTGATTATGAATTTATTTAATGTAAATCCTG 9 69 1 ATTTTTTAAT 0.942549 -124 ATTTAAAGTAATTTTTTTAATCATTTAGACG 9 162 0 ATTTTTTAAT 0.944607 -31 TCTTTATCTAATTTGTTTAATTCTGTTTTTA 11 133 0 ATTTTTTAAT 0.944984 -168 TAAATAATTAATTTTATTAATTAGCATATTT 11 223 1 ATTTATTAAT 0.776629 -78 **** ****** Masking position 1 Map Score: 11.3078 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 171 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 12 ATGGATTTTGAATTTAGGGAAGGCGGCAAGT 2 41 1 AATTAGGGAA 0.962797 -196 TTTGCGTATAGATTGAGCAAATCCCAAATAG 3 105 1 GATTAGCAAA 0.880304 -172 TGGTGAGGAAAAATCAGGGAAGATGAAAAAA 4 161 0 AAATAGGGAA 0.921374 -140 CAGATGTAAAGATGAAGGAAAAGCCGAAGGG 4 216 0 GATGAGGAAA 0.748503 -85 AAGTTAATTTAAATAAGGAAATAT 6 261 1 AAATAGGAAA 0.856414 -14 ATCAATAAGCACTTAAGGGAAATT 7 233 1 ACTTAGGGAA 0.843681 -14 ACGATGAATCAATTCAGCTAACTTATTTCCT 9 16 0 AATTAGCTAA 0.673552 -177 ATTTCTGTTTAATTCAGCGAAAATAAGTTAT 10 24 1 AATTAGCGAA 0.930251 -84 CTCCGTTTTAGATTTAGAAAAACAAACGAAA 10 83 1 GATTAGAAAA 0.649257 -25 ATAAAATTAAGAATTAGGGAACCAGTATAAT 11 267 0 GAATAGGGAA 0.926986 -34 **** ****** Masking position 6 Map Score: 3.05656 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 107 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 13 ********** No masking Map Score: -2.55552e-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: -2.55552e-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 ********** No masking Map Score: -2.55552e-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