AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i055_Arginine_Metabolism_ecoli_hinf_reg_300.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 argF 300 ornithine carbamoyltransferase 2, chain F #2 ackA 300 acetate kinase #3 pta 74 phosphotransacetylase #4 yfcC 168 putative S-transferase #5 argI 161 ornithine carbamoyltransferase 1 #6 HI0594 104 conserved hypothetical transmembrane protein #7 HI0596 300 ornithine carbamoyltransferase (arcB) Motif number 1 TATGCTTCTAAAATGGCGGAGAACATGGCGA 1 40 0 AATGGCGGAG 0.971763 -261 AAGAATTGTGAAATGGGGTTGCAAATGAATA 1 222 1 AATGGGGTTG 0.986773 -79 TTAATTCAATAAGTGGCGTTCGCCATGCGAG 1 274 1 AATGGCGTTC 0.916611 -27 AAATTACGCAAAATGGCATAGACTCAAGATA 2 155 1 AATGGCATAG 0.849781 -146 ATGCAAAAAAAATTTGCAGTGCATGATGTTA 2 197 1 AATTGCAGTG 0.68721 -104 TGTTAATCATAAATGTCGGTGTCATCATGCG 2 223 1 AATGTCGGTG 0.931497 -78 CCGCCAGCTGAGCTGGCGGTGTGAAA 3 6 0 AGTGGCGGTG 0.987265 -69 CCGCCAGCTCAGCTGGCGGTGCTGTTTTGTA 3 18 1 AGTGGCGGTG 0.987265 -57 CGCAGCGCAAAGCTGCGGATGATGACGAGA 4 10 0 AGTGCGGATG 0.771325 -159 TAAGTATGCAAAGTGGGATGGCGCAATTCAT 4 136 0 AATGGGATGG 0.774522 -33 TCAAGGTAAAAAGTGCGGTTGGTTTAACCAA 6 39 1 AATGCGGTTG 0.966735 -66 TTAACGTTTAAAGTGCGGTTGGTAAAACATT 6 68 0 AATGCGGTTG 0.966735 -37 ** ******** Masking position 1 Map Score: 13.7168 Number of sites scoring better than the average of aligned sites = 1563 Number in coding regions = 1474 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 2 TTTATCCTCGCATGGCGAACGCCACTT 1 284 0 TCGCATGGCG 0.970207 -17 TTTCAGCCAATGGCATAATGTATATGAATT 2 127 0 TGGCATAATG 0.855665 -174 CAAATTTTTTTTGCATGATGGAAGAAATAT 2 183 0 TTGCATGATG 0.971688 -118 AAAATTTGCAGTGCATGATGTTAATCATAA 2 205 1 GTGCATGATG 0.971132 -96 ATAGAGCGTAGCGCATGATGACACCGACAT 2 235 0 GCGCATGATG 0.990055 -66 GCGCAAAGCTGCGGATGATGACGAGA 4 7 0 GCGGATGATG 0.976749 -162 GTATGCAAAGTGGGATGGCGCAATTCATTG 4 134 0 TGGGATGGCG 0.877798 -35 AAGCAGTATCTCGAATGATGTATGTTTATT 7 247 1 TCGAATGATG 0.940167 -54 ********** Masking position 5 Map Score: 8.20897 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 460 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 ATGCTTCTAAAATGGCGGAGAACATGGCGA 1 40 0 AATGGCGGAG 0.993679 -261 TCTTTCTTACAAAGGTGGAGGCAAACCCGT 1 196 0 AAAGGTGGAG 0.919105 -105 AGAATTGTGAAATGGGGTTGCAAATGAATA 1 223 1 AATGGGGTTG 0.879971 -78 AATTACGCAAAATGGCATAGACTCAAGATA 2 156 1 AATGGCATAG 0.859058 -145 GTTAATCATAAATGTCGGTGTCATCATGCG 2 224 1 AATGTCGGTG 0.974448 -77 CGCCAGCTGAGCTGGCGGTGTGAAA 3 6 0 GCTGGCGGTG 0.978846 -69 CGCCAGCTCAGCTGGCGGTGCTGTTTTGTA 3 19 1 GCTGGCGGTG 0.978846 -56 AGGTGGAGGCAATGTCAGTGGTGTGTGACA 5 47 0 AATGTCAGTG 0.882482 -115 TCTTTGTCACAAAGGTGGAGGCAATGTCAG 5 59 0 AAAGGTGGAG 0.919105 -103 ********** Masking position 4 Map Score: 8.04208 Number of sites scoring better than the average of aligned sites = 2088 Number in coding regions = 1990 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 AGAATTCGATCCAATGTCTTTCTGCTTCTG 1 127 1 CCAATGTCTT 0.87638 -174 AATGGGGTTGCAAATGAATAATTACACATA 1 233 1 CAAATGAATA 0.888613 -68 ATTTGACGACTCAATGAATATGTACTACTT 2 100 0 TCAATGAATA 0.953748 -201 CTGCGCTGCATCAATGAATTGCGCCATCCC 4 123 1 TCAATGAATT 0.943622 -46 TTTAGACTTGCAAATGAATAATCATCCATA 5 96 1 CAAATGAATA 0.888613 -66 GAATTAAAATTCAATTTATATGGATGATTA 5 114 0 TCAATTTATA 0.621332 -48 GGCTAACGCCTCAATGAATTAAAATTCAAT 5 129 0 TCAATGAATT 0.943622 -33 GTTGGTTTAACCAATGTTTTACCAACCGCA 6 56 1 CCAATGTTTT 0.827086 -49 TGTTTATTCCCCAATGTATAGTCAAAACAC 7 269 1 CCAATGTATA 0.970488 -32 ********** Masking position 5 Map Score: 7.67547 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 178 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 CAAAGGTGGAGGCAAACCCGTCCGTGTGTGAA 1 185 0 GGCAACCGTC 0.984315 -116 ATCCTCGCATGGCGAACGCCACTTATTGAATT 1 276 0 GGCAACCCAC 0.992558 -25 GGCTCATTCCTCTTAATGTCCT 5 1 1 GGCCATCCTC 0.992914 -161 TACTCTTATTGTCACACACCACTGACATTGCC 5 38 1 GTCCACCCAC 0.977924 -124 TCCCTCCTGTGGCTAACGCCTCAATGAATTAA 5 137 0 GGCAACCCTC 0.996348 -25 AGTATAGATAGACACATTCCTCTTCATCAAAA 7 19 1 GACCATCCTC 0.961769 -282 *** *** **** Masking position 6 Map Score: 6.23547 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 88 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 AGCATAATCCTTAAAATCATAAAGAAGGCC 1 65 1 TTAAAATCAT 0.756219 -236 AGACATTGGATCGAATTCTACAACCAGGTC 1 116 0 TCGAATTCTA 0.620743 -185 CTTATTGAATTAAAATTCACTTTATATGTG 1 257 0 TAAAATTCAC 0.920623 -44 CATTGAGTCGTCAAATTCATATACATTATG 2 114 1 TCAAATTCAT 0.880807 -187 CTCAATGAATTAAAATTCAATTTATATGGA 5 120 0 TAAAATTCAA 0.895646 -42 ATATTTTCGTTTAAATTCATCTACTATTAG 7 63 1 TTAAATTCAT 0.87036 -238 CATCTACTATTAGAAATCAAACAAATAACA 7 80 1 TAGAAATCAA 0.712953 -221 GATTATTTTATTAAATTCTAATAATACTAA 7 121 1 TTAAATTCTA 0.786615 -180 CTAATAATACTAAAAATCTCGCAATAAAAT 7 138 1 TAAAAATCTC 0.785823 -163 AATCTCGCAATAAAATTCTACATACTGGCA 7 152 1 TAAAATTCTA 0.849109 -149 ********** Masking position 5 Map Score: 5.34082 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 169 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 TAATGAAGTAAGGCAGCAAGCCTCGCCATG 1 18 1 AGGCAGCAAG 0.822569 -283 TAATCCTTAAAATCATAAAGAAGGCCAATC 1 69 1 AATCATAAAG 0.916784 -232 AACCAGGTCGAGTCAGAAATGAGAATGATT 1 95 0 AGTCAGAAAT 0.927339 -206 TTCTCTGCAGAAGCAGAAAGACATTGGATC 1 134 0 AAGCAGAAAG 0.975958 -167 GCATGATGTTAATCATAAATGTCGGTGTCA 2 217 1 AATCATAAAT 0.895359 -84 CGGATATCTGAACCGGAAATAATCACTATT 4 39 1 AACCGGAAAT 0.91365 -130 GAGAATAAAAAACCGGAAATAGTGATTATT 4 56 0 AACCGGAAAT 0.91365 -113 TAAGCAAGATAATCAGAAAGGATTAATGCA 4 92 0 AATCAGAAAG 0.971111 -77 TGCAAGTCTAAAGCATAAATCTTTGTCACA 5 78 0 AAGCATAAAT 0.911767 -84 ********** Masking position 8 Map Score: 7.58373 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 270 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 8 ATAATTACACATATAAAGTGAATTTTAATT 1 250 1 ATATAAAGTG 0.727516 -51 GGATTAATGCAAATTAAGAGAATAAAAAAC 4 73 0 AAATTAAGAG 0.91991 -96 AAAACAAAGTGGTAAGTATGC 4 158 0 AAACAAAGTG 0.819482 -11 TATCGGCAGGACATTAAGAGGAATGAGCC 5 10 0 ACATTAAGAG 0.959554 -152 GTGGTGTGTGACAATAAGAGTATCGGCAGG 5 30 0 ACAATAAGAG 0.85408 -132 TAAACGTTAAACATAAGGAGCTCGCT 6 89 1 ACATAAGGAG 0.955659 -16 AAACAAATAACAATAAAGAGTTAGATTATT 7 98 1 CAATAAAGAG 0.830342 -203 TATAGTCAAAACACAAGGAGATTATT 7 285 1 ACACAAGGAG 0.935496 -16 ********** Masking position 6 Map Score: 2.73531 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 108 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 GCTCCCTGACGTTTTTTTAGCCACGTATCAATTA 2 266 1 GTTTTACCAC 0.974734 -35 TGGCGGTGCTGTTTTGTAACCCGCCAAATCGGCG 3 31 1 GTTTTACCGC 0.995063 -44 ATTATTTCCGGTTCAGATATCCGCAGCGCAAAGC 4 28 0 GTTCAACCGC 0.988024 -141 TAAAACATTGGTTAAACCAACCGCACTTTTTACC 6 43 0 GTTAAACCGC 0.982352 -62 TTTAACCAATGTTTTACCAACCGCACTTTAAACG 6 61 1 GTTTTACCGC 0.995062 -44 ***** * **** Masking position 9 Map Score: 2.24411 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 45 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 CTACAACCAGGTCGAGTCAGAAATGAGAAT 1 99 0 GTCGAGTCAG 0.931515 -202 CCGATTCTCTGCAGAAGCAGAAAGACATTG 1 138 0 GCAGAAGCAG 0.881225 -163 CTGCAGAGAATCGGAGGCAGATACGATTAT 1 154 1 TCGGAGGCAG 0.921049 -147 TCTTACAAAGGTGGAGGCAAACCCGTCCGT 1 192 0 GTGGAGGCAA 0.984773 -109 GACAATAAGAGTATCGGCAGGACATTAAGA 5 21 0 GTATCGGCAG 0.877072 -141 TGTCACAAAGGTGGAGGCAATGTCAGTGGT 5 55 0 GTGGAGGCAA 0.984773 -107 ATTCCCCAATGTATAGTCAAAACACAAGGA 7 274 1 GTATAGTCAA 0.75386 -27 ********** Masking position 9 Map Score: 0.839168 Number of sites scoring better than the average of aligned sites = 1009 Number in coding regions = 950 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 11 ********** No masking Map Score: 1.15351e-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 ATGATTTTAAGGATTATGCTTCTAAAATGGCG 1 53 0 GGTATGCTTC 0.952597 -248 CACTTTATATGTGTAATTATTCATTTGCAACC 1 238 0 GTTATTATTC 0.913687 -63 CATAGACTCAAGATATTTCTTCCATCATGCAA 2 171 1 AGTTTTCTTC 0.867194 -130 CACTATTTCCGGTTTTTTATTCTCTTAATTTG 4 62 1 GGTTTTATTC 0.976566 -107 GGCTCATTCCTCTTAATGTCCT 5 1 1 GGTATTCCTC 0.952713 -161 CAATTTATATGGATGATTATTCATTTGCAAGT 5 101 0 GGTATTATTC 0.97788 -61 CTCGAATGATGTATGTTTATTCCCCAATGTAT 7 256 1 GTTTTTATTC 0.919014 -45 ** * ******* Masking position 7 Map Score: 2.67051 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 131 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 13 ********** No masking Map Score: 1.15351e-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: 1.15351e-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: 1.15351e-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