AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 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 Motif number 1 AAGAATAAAAAACGCAATGTTATGCAGAAGTAAAAT 1 70 0 AGAATTATCA 0.982981 -231 ATTCACCCACATCGCAAACGTATTCACTTTATATGC 1 109 1 AGAAAGATCA 0.935651 -192 ATGAAAGTGAACTGGATATTCATTCACATGATTAGC 2 94 0 AGATATATCA 0.982981 -207 AGAGCAGGAGAAGGCAAAAGTATTCAACAAATGAAA 2 124 0 AGAAAGATCA 0.935651 -177 CTCTCCCTTAAGCGCATTATTTTACAAAAAACACAC 2 156 1 AGATTTTTCA 0.94685 -145 AAGATGATTAAATGAAAACTCATTTATTTTGCATAA 2 215 1 AGAAATATTA 0.750642 -86 TTCCGCTCTCACTGAATTTTTATGCAAAATAAATGA 2 234 0 AGATTTATCA 0.987579 -67 ATTGCCATTTAGTGATTTTTTATGCATATTTTGTGG 3 17 1 AGTTTTATCA 0.902051 -69 GCTCAACGTTAGTGTATTTTTATTCATAAATACTGC 6 50 0 AGATTTATCA 0.987579 -104 AGTGTGATGTAACGCAATCTGTTACATAACGAATTG 8 63 0 AGAATTTTCA 0.928267 -238 TAGACTTGCAAATGAATAATCATCCATATAAATTGA 9 98 1 AGATATATCA 0.982981 -64 ATCCATATAAATTGAATTTTAATTCATTGAGGCGTT 9 119 1 AGATTTATCA 0.987579 -43 * * *** * ** ** Masking position 1 Map Score: 19.178 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 36 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 TCAGAATGGCGCAGTAATTTCCAGTAAATTTCG 1 12 1 GAGAATTTCA 0.909058 -289 ATGTTATGCAGAAGTAAAATATAATTCTGGAAT 1 57 0 GAGAAAATTA 0.735253 -244 CTAATCATGTGAATGAATATCCAGTTCACTTTC 2 95 1 GATAATATCA 0.980504 -206 TCCCTTAAGCGCATTATTTTACAAAAAACACAC 2 159 1 GATATTTTCA 0.800248 -142 CATTTATTTTGCATAAAAATTCAGTGAGAGCGG 2 235 1 GATAAAATCA 0.985762 -66 CACAAAATATGCATAAAAAATCACTAAATGGCA 3 19 0 GATAAAAACA 0.889126 -67 GGTCATGATAGTATCAATATTCATGCAGTATTT 6 26 1 GATAATATCA 0.980504 -128 CAGTATTTATGAATAAAAATACACTAACGTTGA 6 51 1 GATAAAATCA 0.985762 -103 CAGCTTTCCGGCATTGAATTTCAAAATAAGGAA 7 30 1 GATGAATTCA 0.808637 -31 GGTATACAGAGCAGGAAAATCCATAACCGTAGC 8 165 0 GAGAAAATCA 0.974815 -136 CAATTTATATGGATGATTATTCATTTGCAAGTC 9 100 0 GATATTATCA 0.918486 -62 ACGCCTCAATGAATTAAAATTCAATTTATATGG 9 121 0 GATAAAATCA 0.985762 -41 * ** ***** ** Masking position 3 Map Score: 18.736 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 72 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 GTGGGTGAATAAAAAGAATAAAAAACGCAA 1 89 0 AAAAAGAATA 0.646137 -212 AAGTGCATATAAAGTGAATACGTTTGCGAT 1 119 0 AAAGTGAATA 0.974358 -182 ATATGCATTTAAAGTGCATATAAAGTGAAT 1 130 0 AAAGTGCATA 0.942324 -171 GCCAGTGATAAAAGTGCATAAACGGCGGAG 1 193 0 AAAGTGCATA 0.942324 -108 AGCGACCTCTACAGTAAATAATTCGTTATT 1 281 0 ACAGTAAATA 0.771781 -20 ATTTTTATGCAAAATAAATGAGTTTTCATT 2 225 0 AAAATAAATG 0.66621 -76 CACCAGCCGTAAGGTGAATGTTTTACGTTT 6 97 1 AAGGTGAATG 0.950649 -57 CAGACATAAGAAGGTGAATAGCCCCG 6 138 1 AAGGTGAATA 0.964355 -16 ACACTTCAAAAAAGTAAATAAAACGTTAAT 8 94 1 AAAGTAAATA 0.941913 -207 ACTGGTGAAAAAGGAAAATGAAGACGAAAA 8 206 1 AAGGAAAATG 0.695598 -95 ********** Masking position 8 Map Score: 8.29375 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 239 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 TAAATTTCGTCAATGATCACAATTCCAGAAT 1 36 1 CATGATCACA 0.785525 -265 CGTTTATGCACTTTTATCACTGGCTGGCACG 1 199 1 CTTTATCACT 0.750636 -102 AAATGTGAAATTATAACCACAAAATATGCAT 3 38 0 TATAACCACA 0.803596 -48 TGAACGTGTCCATTTGCCACAAGTATAAGCG 5 72 0 CTTTGCCACA 0.979716 -33 GTAAATAAAACGTTAATCACAAGTTTGTAAT 8 107 1 CTTAATCACA 0.922489 -194 ACTCGGCACTTGTTTGCCACATATTTTTAAA 8 270 1 TTTTGCCACA 0.960903 -31 GCCGATACTCTTATTGTCACACACCACTGAC 9 33 1 TATTGTCACA 0.909228 -129 AAAGCATAAATCTTTGTCACAAAGGTGGAGG 9 68 0 TTTTGTCACA 0.950237 -94 TTCATTGAGGCGTTAGCCACAGGAGGGATCT 9 141 1 CTTAGCCACA 0.967848 -21 * ********* Masking position 4 Map Score: 6.12215 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 231 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 TAATAAGTAATGTTTGCGCTGTAAATGTAG 1 241 0 TGTTTGCGCT 0.884689 -60 TGCCTTCTCCTGCTCTCCCTTAAGCGCATT 2 144 1 TGCTCTCCCT 0.973419 -157 CGGGCAAGATTGCCCGCGCGAGAAATCA 5 9 0 TGCCCGCGCG 0.989997 -96 CGGGCAATCTTGCCCGCGCTTCTGCTCTCC 5 23 1 TGCCCGCGCT 0.98859 -82 CCCGCGCTTCTGCTCTCCCGGCGTAACCCG 5 35 1 TGCTCTCCCG 0.977887 -70 TCGCGCCGAATGTCTTCGCTTGTTTTCGTC 8 228 0 TGTCTTCGCT 0.929188 -73 TTCCTCTTAATGTCCTGCCGATACTCTTAT 9 17 1 TGTCCTGCCG 0.894753 -145 ********** Masking position 1 Map Score: 5.15449 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 675 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 GTAAAATAATGCGCTTAAGGGAGAGCAGGA 2 151 0 GCGCTTAAGG 0.948895 -150 GGCGGCTCCGGTACAAAAGAA 4 21 0 GCGGCTCCGG 0.993846 -11 CCGGAAAGCTGCGCCTCCGGCCAACAAAAC 7 11 0 GCGCCTCCGG 0.997454 -50 TATGAAAAATGCGGCTACGGTTATGGATTT 8 152 1 GCGGCTACGG 0.996255 -149 ********** Masking position 6 Map Score: 4.5153 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 7 ATCATGTGAATGAATATCCAGTTCACTTTC 2 98 1 TGAATATCCA 0.654754 -203 GCAAAATAAATGAGTTTTCATTTAATCATC 2 217 0 TGAGTTTTCA 0.885693 -84 CCGCTCTCACTGAATTTTTATGCAAAATAA 2 238 0 TGAATTTTTA 0.939416 -63 TGCCATTTAGTGATTTTTTATGCATATTTT 3 19 1 TGATTTTTTA 0.872357 -67 AAATACTGCATGAATATTGATACTATCATG 6 29 0 TGAATATTGA 0.691489 -125 TCAACGTTAGTGTATTTTTATTCATAAATA 6 54 0 TGTATTTTTA 0.746571 -100 TTTCCGGCATTGAATTTCAAAATAAGGAAA 7 34 1 TGAATTTCAA 0.864268 -27 TTTATATGGATGATTATTCATTTGCAAGTC 9 100 0 TGATTATTCA 0.643545 -62 CCATATAAATTGAATTTTAATTCATTGAGG 9 121 1 TGAATTTTAA 0.919239 -41 ********** Masking position 5 Map Score: 3.95458 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 125 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 8 TGGCTGGCACGAACCCTGCAATCTACATTT 1 219 1 GAACCCTGCA 0.96416 -82 CGGTACACCAAATCCCAGCAG 2 2 0 AATCCCAGCA 0.957039 -299 GGATCACTATAATGCCTGCAGATTTTACGT 2 39 0 AATGCCTGCA 0.974992 -262 TTGATGCCTCCCTGAACGTGTC 5 93 0 GATGCCTCCC 0.957647 -12 GAGCGTAATAAAACCCACCAGCCGTAAGGT 6 82 1 AAACCCACCA 0.927162 -72 CACCACTGACATTGCCTCCACCTTTGTGAC 9 54 1 ATTGCCTCCA 0.914024 -108 AGATCCCTCCTGTGGCTAACG 9 151 0 GATCCCTCCT 0.952467 -11 ********** Masking position 5 Map Score: 2.4051 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 233 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 9 TATTCAACAAATGAAAGTGAACTGGATATT 2 110 0 ATGAAAGTGA 0.942921 -191 TTTCAAAATAAGGAAACAGAGTT 7 48 1 AGGAAACAGA 0.981889 -13 ACAATTCGTTATGTAACAGATTGCGTTACA 8 62 1 ATGTAACAGA 0.894806 -239 TCATAGTGAGATGAAAGCGATTACAAACTT 8 127 0 ATGAAAGCGA 0.932817 -174 CTGGTGAAAAAGGAAAATGAAGACGAAAAC 8 207 1 AGGAAAATGA 0.904973 -94 ATATTTTTAAAGGAAACAGAC 8 290 1 AGGAAACAGA 0.981889 -11 ********** Masking position 5 Map Score: 2.90757 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 110 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 AAACGTTGACAAAATGTGGCGTGGATCACT 2 61 0 AAAATGTGGC 0.966863 -240 TTGCCACAAGTATAAGCGGCAAATCCGGGT 5 60 0 TATAAGCGGC 0.918908 -45 CTCACTATGAAAAATGCGGCTACGGTTATG 8 147 1 AAAATGCGGC 0.985017 -154 AGTTGGCTATAATACTCGGCACTTGTTTGC 8 257 1 AATACTCGGC 0.913708 -44 TTCCTTTAAAAATATGTGGCAAACAAGTGC 8 275 0 AATATGTGGC 0.976641 -26 ********** Masking position 4 Map Score: 0.985726 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 180 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 AAAATAACACCCTGCTTAATTAACTGATG 2 282 0 CACCCTCTAA 0.969558 -19 CGCTTCTGCTCTCCCGGCGTAACCCGGATTTG 5 39 1 CTCCCGCTAA 0.98059 -66 TAATAAAACCCACCAGCCGTAAGGTGAATGTT 6 87 1 CACCAGCTAA 0.993547 -67 TTAACCTGGCAACCAGACATAAGAAGGTGAAT 6 125 1 AACCAGCTAA 0.967218 -29 TTTCCTTTTTCACCAGTTTTAAGACGGTATAC 8 191 0 CACCAGTTAA 0.967218 -110 ****** * *** Masking position 10 Map Score: 0.923399 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 78 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 ACGAAATTTACTGGAAATTACTGCGCCATT 1 16 0 CTGGAAATTA 0.879928 -285 CGGAGGCTAACTGGAAATCAAGGAGTTATA 1 168 0 CTGGAAATCA 0.982608 -133 AAATCACTAAATGGCAATCAGAAA 3 5 0 ATGGCAATCA 0.947512 -81 ATTGCCCGCGCGAGAAATCA 5 1 0 CGAGAAATCA 0.831403 -104 ATTTCTCGCGCGGGCAATCTTGCCCGCGCT 5 13 1 CGGGCAATCT 0.942201 -92 TACGTTTAACCTGGCAACCAGACATAAGAA 6 120 1 CTGGCAACCA 0.977099 -34 TTAAAAATATGTGGCAAACAAGTGCCGAGT 8 270 0 GTGGCAAACA 0.868431 -31 ********** Masking position 6 Map Score: 2.43546 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 900 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 13 ********** No masking Map Score: 2.17669e-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: 2.17669e-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: 2.17669e-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