AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 cstC 300 acetylornithine delta-aminotransferase #2 argG 300 argininosuccinate synthetase #3 argD 85 acetylornithine delta-aminotransferase #4 pabA 31 p-aminobenzoate synthetase, component II #5 yhfG 104 orf, hypothetical protein #6 argC 153 N-acetyl-gamma-glutamylphosphate reductase #7 argH 60 argininosuccinate lyase #8 ppa 300 inorganic pyrophosphatase #9 argI 161 ornithine carbamoyltransferase 1 #10 HI0124 234 inorganic pyrophosphatase (ppa) #11 HI0596 300 ornithine carbamoyltransferase (arcB) #12 HI0811 134 argininosuccinate lyase (argH) #13 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 TTTTTTATTCTTTTTATTCACCCACATCGC 1 94 1 TTTTTATTCA 0.971414 -207 ACGTATTCACTTTATATGCACTTTAAATGC 1 126 1 TTTATATGCA 0.931455 -175 TTATATGCACTTTAAATGCATATGGTTTGG 1 137 1 TTTAAATGCA 0.885723 -164 GTGAACTGGATATTCATTCACATGATTAGC 2 94 0 TATTCATTCA 0.820351 -207 TCTCACTGAATTTTTATGCAAAATAAATGA 2 234 0 TTTTTATGCA 0.982029 -67 ATTTAGTGATTTTTTATGCATATTTTGTGG 3 23 1 TTTTTATGCA 0.982029 -63 ATAGTATCAATATTCATGCAGTATTTATGA 6 33 1 TATTCATGCA 0.880138 -121 CGTTAGTGTATTTTTATTCATAAATACTGC 6 50 0 TTTTTATTCA 0.971414 -104 ATAAATTGAATTTTAATTCATTGAGGCGTT 9 125 1 TTTTAATTCA 0.950937 -37 CATATTTTCGTTTAAATTCATCTACTATTA 11 62 1 TTTAAATTCA 0.828179 -239 TTTACCTCTCTTATAATGCAACTGTTCGAA 11 213 1 TTATAATGCA 0.727281 -88 TTATTGTGCATATTTATTCATAAAGCAATA 12 82 0 TATTTATTCA 0.922468 -53 AAATTAGGATTTTTTATGCACAAAGCTAAA 13 11 1 TTTTTATGCA 0.982029 -145 AGATTTTTGCTTTTAATGCACAAAACACTA 13 44 1 TTTTAATGCA 0.968912 -112 CTCTATAGAATTTTTATTCACAAAAATCGA 13 99 1 TTTTTATTCA 0.971414 -57 AAAAATCGATTATTTATTCAATTCTAATTA 13 120 1 TATTTATTCA 0.922468 -36 ********** Masking position 6 Map Score: 32.4025 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 110 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 TGGGTGAATAAAAAGAATAAAAAACGCAATGTTA 1 84 0 AAAAGAAAAA 0.942564 -217 AGCCAGTGATAAAAGTGCATAAACGGCGGAGGCT 1 190 0 AAAAGTAAAC 0.807797 -111 GATTAGCAATAAACGTTGACAAAATGTGGCGTGG 2 67 0 AAACGTAAAA 0.906775 -234 TTATTTTACAAAAAACACACTAAACTCTTCCTGT 2 172 1 AAAAACAAAA 0.764445 -129 TGTCTCCGATAAAAGATGATTAAATGAAAACTCA 2 203 1 AAAAGAAAAA 0.942564 -98 AAATATGCATAAAAAATCACTAAATGGCAATCAG 3 14 0 AAAAAAAAAA 0.93284 -72 ATTTATGAATAAAAATACACTAACGTTGAGCGTA 6 55 1 AAAAATAAAC 0.780569 -99 CACACTTCAAAAAAGTAAATAAAACGTTAATCAC 8 93 1 AAAAGTAAAA 0.953184 -208 TGAAAAAGGAAAATGAAGACGAAAACAAGCGAAG 8 211 1 AAATGAAAAA 0.60037 -90 AGTGTTCCTTGAAGTTAAGTAAAAAATTGGAAG 10 10 1 TGAAGTAAAA 0.648512 -225 TACATCATAAAAACGATAAGTAAACGTTTGCGTG 10 62 1 AAACGAAAAA 0.886877 -173 TCATTTGTAGAGAAAATCAGCAAATAGATCCATC 10 142 0 AGAAAAAAAA 0.861154 -93 TTTAACTTGATAAAATGAAGGAAACAAA 10 217 1 TAAAATAAAA 0.777644 -18 CCTCTTCATCAAAAATAAACTAAAACATATTTTC 11 37 1 AAAAATAAAA 0.945154 -264 ATCTACTATTAGAAATCAAACAAATAACAATAAA 11 81 1 AGAAATAAAA 0.88499 -220 CTAATACAAATAAAATGGACAAAATGAAAGATTT 12 17 1 TAAAATAAAA 0.777644 -118 ATAATAAAACAAAAATGGACAAAATCTTTCATTT 12 38 0 AAAAATAAAA 0.945154 -97 TAATTAATTAAAACAAAAAGGAAAAATT 12 117 1 AAACAAAAAA 0.869035 -18 ACAAAACACTAGACAAAGAGGAAAAGTGCGGTTA 13 63 1 AGACAAAAAA 0.747665 -93 ****** * *** Masking position 9 Map Score: 19.3634 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 215 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 GTCAGAATGGCGCAGTAATTTCCAGTAAATTTCGTCA 1 11 1 CGCATTTCAA 0.97922 -290 GAATAAAAAACGCAATGTTATGCAGAAGTAAAATATA 1 67 0 CGCATATCAA 0.985821 -234 TCACCCACATCGCAAACGTATTCACTTTATATGCACT 1 111 1 CGCAAATCAT 0.89105 -190 AGCAGGAGAAGGCAAAAGTATTCAACAAATGAAAGTG 2 121 0 GGCAAATCAA 0.960173 -180 CTCCCTTAAGCGCATTATTTTACAAAAAACACACTAA 2 158 1 CGCATTTCAA 0.97922 -143 CCGCTCTCACTGAATTTTTATGCAAAATAAATGAGTT 2 231 0 TGAATATCAA 0.666701 -70 GCAGCTTTCCGGCATTGAATTTCAAAATAAGGAAACA 7 29 1 GGCATTTCAA 0.960173 -32 TGTGATGTAACGCAATCTGTTACATAACGAATTGTCT 8 60 0 CGCATTTCAA 0.97922 -241 TATAATACTCGGCACTTGTTTGCCACATATTTTTAAA 8 264 1 GGCATTTCCA 0.791775 -37 ATAAAACTCACGCAAACGTTTACTTATCGTTTTTATG 10 67 0 CGCAATTCTT 0.509847 -168 ATAGATCCATCTCATAACTATTCATAATTTTGACCGC 10 116 0 CTCAAATCAA 0.727251 -119 CTAAAAATCTCGCAATAAAATTCTACATACTGGCATT 11 147 1 CGCATATCTA 0.928807 -154 TATACATTGGGGAATAAACATACATCATTCGAGATAC 11 252 0 GGAAAATCAA 0.800488 -49 TCTATTATTGTGCATATTTATTCATAAAGCAATATTC 12 79 0 TGCAAATCAA 0.890666 -56 TATACTCTATAGAATTTTTATTCACAAAAATCGATTA 13 95 1 AGAATATCAA 0.531479 -61 **** * ** ** * Masking position 4 Map Score: 11.9484 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 396 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 4 ATATCCAGTTCACTTTCATTTGTTGAATACT 2 111 1 CATTTCATTT 0.929611 -190 AAAATAAATGAGTTTTCATTTAATCATCTTT 2 214 0 AGTTTCATTT 0.807564 -87 AACTCTGTTTCCTTATTTTGAAATT 7 46 0 CTTTTCCTTA 0.712546 -15 AGTTTGTAATCGCTTTCATCTCACTATGAAA 8 128 1 CGTTTCATCT 0.85492 -173 TTTTCGTCTTCATTTTCCTTTTTCACCAGTT 8 205 0 CATTTCCTTT 0.954943 -96 GTCTGTTTCCTTTAAAAATATGT 8 288 0 CTTTTCCTTT 0.961811 -13 GGCTCATTCCTCTTAATGTCCTG 9 3 1 CTATTCCTCT 0.830146 -159 TATATGGATGATTATTCATTTGCAAGTCTAA 9 97 0 ATATTCATTT 0.68443 -65 TGCGAACTCGCAGTCTCATTTGTAGAGAAAA 10 160 0 CATCTCATTT 0.658297 -75 TATAGATAGACACATTCCTCTTCATCAAAAA 11 21 1 CAATTCCTCT 0.804415 -280 AAACGACAACAAATTTCATTTTACCTCTCTT 11 194 1 AATTTCATTT 0.861773 -107 AATGGACAAAATCTTTCATTTTGTCCATTTT 12 28 0 ATTTTCATTT 0.881106 -107 AATTTTTCCTTTTTGTTTTAAT 12 123 0 ATTTTCCTTT 0.922438 -12 GTATAACCGCACTTTTCCTCTTTGTCTAGTG 13 69 0 ACTTTCCTCT 0.708155 -87 ** ******** Masking position 6 Map Score: 8.58372 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 267 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 TTTACTGGAAATTACTGCGCCATTCTGAC 1 10 0 ATTACTGCGC 0.747908 -291 GATTTCCAGTTAGCCTCCGCCGTTTATGCA 1 179 1 TAGCCTCCGC 0.860301 -122 GCAATCTACATTTACAGCGCAAACATTACT 1 236 1 TTTACAGCGC 0.822788 -65 ACTTTTGCCTTCTCCTGCTCTCCCTTAAGC 2 139 1 TCTCCTGCTC 0.806227 -162 GCGGGCAAGATTGCCCGCGCGAGAAATCA 5 10 0 TTGCCCGCGC 0.991031 -95 GCGGGCAATCTTGCCCGCGCTTCTGCTCTC 5 22 1 TTGCCCGCGC 0.991031 -83 GGTTATGGATTTTCCTGCTCTGTATACCGT 8 170 1 TTTCCTGCTC 0.939993 -131 ACCACTGACATTGCCTCCACCTTTGTGACA 9 55 1 TTGCCTCCAC 0.903607 -107 ATTCATAATTTTGACCGCACTTTATCCTAA 10 104 0 TTGACCGCAC 0.908145 -131 ********** Masking position 5 Map Score: 4.80975 Number of sites scoring better than the average of aligned sites = 1667 Number in coding regions = 1575 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 AATGGCGCAGTAATTTCCAGTAAATTTCGTCA 1 16 1 TATTCCAGTA 0.8915 -285 TATAACTCCTTGATTTCCAGTTAGCCTCCGCC 1 168 1 TATTCCAGTT 0.983165 -133 TCATGTGAATGAATATCCAGTTCACTTTCATT 2 99 1 GATTCCAGTT 0.961702 -202 AAATCCAGGCTCATCATCAGTTAATTAAGCAG 2 268 1 TATATCAGTT 0.777039 -33 AATAAAACGTTAATCACAAGTTTGTAATCGCT 8 110 1 TATACAAGTT 0.87335 -191 TCATTTTCCTTTTTCACCAGTTTTAAGACGGT 8 195 0 TTTACCAGTT 0.964598 -106 GTTTCCTTCATTTTATCAAGTTAAAAAACGCA 10 210 0 TTTTCAAGTT 0.873351 -25 CTACATACTGGCATTACCAGTTGAAAAACGAC 11 169 1 GATACCAGTT 0.94491 -132 AAATCTTTCATTTTGTCCATTTTATTTGTATT 12 19 0 TTTTCCATTT 0.87335 -116 AAATGAAAGATTTTGTCCATTTTTGTTTTATT 12 38 1 TTTTCCATTT 0.87335 -97 * ** ******* Masking position 4 Map Score: 5.42276 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 471 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 TCCTGCTCTCCCTTAAGCGCATTATTTTAC 2 151 1 CCTTAAGCGC 0.917205 -150 TTCTTTTGTACCGGAGCCGCC 4 21 1 CCGGAGCCGC 0.993954 -11 GTTTTGTTGGCCGGAGGCGCAGCTTTCCGG 7 11 1 CCGGAGGCGC 0.996111 -50 AAATCCATAACCGTAGCCGCATTTTTCATA 8 152 0 CCGTAGCCGC 0.994109 -149 ********** Masking position 5 Map Score: 2.73568 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 42 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 8 AATTCGTTATTTATATGTTAATAATAAGTAATGTT 1 257 0 TTTTAATAAT 0.97056 -44 TTTGTCAACGTTTATTGCTAATCATGTGAATGAAT 2 78 1 TTTTAATCAT 0.947539 -223 AATAAATGAGTTTTCATTTAATCATCTTTTATCGG 2 208 0 TTATAATCAT 0.769879 -93 TTTATGCATATTTTGTGGTTATAATTTCACATTTG 3 35 1 TTTTTATAAT 0.855241 -51 TGTTATTTGTTTGATTTCTAATAGTAGATGAATTT 11 75 0 TTTTAATAGT 0.897471 -226 GATTATTTTATTAAATTCTAATAATACTAAAAATC 11 121 1 TTTTAATAAT 0.970557 -180 TAAAGCAATATTCTATATTAATAATAAAACAAAAA 12 57 0 TTTTAATAAT 0.970557 -78 ATATTTTCCTTACTAATAATTAGAATTGAA 13 136 0 TTTTAATAAT 0.970479 -20 ** * ******* Masking position 11 Map Score: 3.61679 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 25 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 ATGTTATGCAGAAGTAAAATATAATTCTGG 1 60 0 GAAGTAAAAT 0.96862 -241 ACCGAGACGGGACGTAAAATCTGCAGGCAT 2 28 1 GACGTAAAAT 0.962886 -273 ACGCCTCAATGAATTAAAATTCAATTTATA 9 124 0 GAATTAAAAT 0.855384 -38 TCGTTTTTATGATGTAAAATAGCGCACCTT 10 48 0 GATGTAAAAT 0.945959 -187 CATTATAAGAGAGGTAAAATGAAATTTGTT 11 201 0 GAGGTAAAAT 0.962886 -100 ********** Masking position 5 Map Score: 2.18595 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 29 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 AACGTGTCCATTTGCCACAAGTATAAGCGGC 5 70 0 TTTGCCACAG 0.974206 -35 AAATAAAACGTTAATCACAAGTTTGTAATCG 8 109 1 TTAATCACAG 0.797819 -192 TCGGCACTTGTTTGCCACATATTTTTAAAGG 8 272 1 TTTGCCACAA 0.969512 -29 CGATACTCTTATTGTCACACACCACTGACAT 9 35 1 ATTGTCACAA 0.849116 -127 AGCATAAATCTTTGTCACAAAGGTGGAGGCA 9 66 0 TTTGTCACAA 0.682117 -96 CATTGAGGCGTTAGCCACAGGAGGGATCT 9 143 1 TTAGCCACAG 0.96856 -19 TATAGAATTTTTATTCACAAAAATCGATTAT 13 102 1 TTATTCACAA 0.765095 -54 ********* * Masking position 7 Map Score: 1.62912 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 44 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 AAAAAGAATAAAAAACGCAATGTTATGCAG 1 79 0 AAAAACGCAA 0.838761 -222 GGTTGCCAGGTTAAACGTAAAACATTCACC 6 109 0 TTAAACGTAA 0.606327 -45 AAAAAGTAAATAAAACGTTAATCACAAGTT 8 102 1 TAAAACGTTA 0.728315 -199 TTTGCAAGTCTAAAGCATAAATCTTTGTCA 9 80 0 TAAAGCATAA 0.601955 -82 TTTACATCATAAAAACGATAAGTAAACGTT 10 60 1 AAAAACGATA 0.811366 -175 TATCAAGTTAAAAAACGCAACAAGTATAGC 10 199 0 AAAAACGCAA 0.838761 -36 GTAGATGAATTTAAACGAAAATATGTTTTA 11 57 0 TTAAACGAAA 0.794534 -244 TTACCAGTTGAAAAACGACAACAAATTTCA 11 182 1 AAAAACGACA 0.716154 -119 ATAAGAGAGGTAAAATGAAATTTGTTGTCG 11 197 0 TAAAATGAAA 0.554972 -104 ATATTAATAATAAAACAAAAATGGACAAAA 12 48 0 TAAAACAAAA 0.882679 -87 TATTTATTCATAAAGCAATATTCTATATTA 12 72 0 TAAAGCAATA 0.574521 -63 AATAATTAATTAAAACAAAAAGGAAAAATT 12 115 1 TAAAACAAAA 0.882679 -20 TTTGTGCATTAAAAGCAAAAATCTTTATTT 13 38 0 AAAAGCAAAA 0.708195 -118 ********** Masking position 4 Map Score: 3.89152 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 418 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 12 TAATGCGCTTAAGGGAGAGCAGGAGAAGGC 2 145 0 AAGGGAGAGC 0.956331 -156 TTATCGGAGACAGGAAGAGTTTAGTGTGTT 2 185 0 CAGGAAGAGT 0.926277 -116 CATAAAAATTCAGTGAGAGCGGAAATCCAG 2 246 1 CAGTGAGAGC 0.956331 -55 TTATGCGTAACAGGGTGATCATGAG 3 71 1 CAGGGTGATC 0.944355 -15 CCGGGTTACGCCGGGAGAGCAGAAGCGCGG 5 36 0 CCGGGAGAGC 0.981114 -69 GTATACAGAGCAGGAAAATCCATAACCGTA 8 167 0 CAGGAAAATC 0.743097 -134 AGTCAAAACACAAGGAGATTATT 11 288 1 CAAGGAGATT 0.743097 -13 ********** Masking position 8 Map Score: 0.666023 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 428 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 ********** No masking Map Score: -4.35319e-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: -4.35319e-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: -4.35319e-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