AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i015_Glycolysis_2_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 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #2 pykA 127 pyruvate kinase II, glucose stimulated #3 pfkA 180 6-phosphofructokinase I #4 HI0982 95 6-phosphofructokinase (pfkA) #5 HI0985 300 DNA processing chain A (dprA) Motif number 1 CCAACGTGAGTGCCTGTTTTTGAGTCGTTGAGTTCT 1 118 0 TGCTTTTAGC 0.987072 -183 GAGGAATGTGTGCTTGTGTCTCAGCCCAACGTGAGT 1 143 0 TGTTTCTAGC 0.925381 -158 CGACTGTCACTGTCCTAATCTTATACGACATCCGAA 2 14 1 TGCATCTATC 0.976028 -114 ATCGCCATCGCGGCGTTATTTCATTCGGATTTCATG 2 62 1 CGCTTTTATC 0.976464 -66 AATGCGGGTCTGGCTCTCTTTTATACTGA 3 4 0 TGCTTTTATC 0.993639 -177 TCAGGCCAAATGGCGGTATTTTATACACAAAATGCG 3 34 0 TGCTTTTATC 0.993639 -147 ATTCTTTGAATGATGTAATCTTATGCCCATTTTCAA 4 47 1 TGTATCTATC 0.889102 -49 ATAGTTTGACAGCCAGTTTTTTATTC 5 1 0 AGCTTTTATC 0.965509 -300 AAGAAAAATTTTGCAATTTTTTATTCATTAAAAAGA 5 182 1 TTCTTTTATC 0.9387 -119 ** * * *** ** * Masking position 9 Map Score: 9.57441 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 147 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 TTTTGTTTTCCTTTTGGATTAATTTCAGCG 1 39 1 CTTTTGGATT 0.782977 -262 CCTCTGCACGCTTTTTCGATGTCACCTATC 1 175 1 CTTTTTCGAT 0.886594 -126 AACAGATTTCATTTTGCATTCCAAAGTTCA 3 152 1 ATTTTGCATT 0.925917 -29 GTCAAACTATTTTTTGGCATTTTATATTAA 5 27 1 TTTTTGGCAT 0.904571 -274 CTTATTGGATTTTTTACATTTTCAAAATAA 5 154 1 TTTTTACATT 0.722279 -147 AATAAGAAAAATTTTGCAATTTTTTATTCA 5 179 1 ATTTTGCAAT 0.948135 -122 TTAAAAAGAATTTTTGCGATCTGCATCGCA 5 209 1 TTTTTGCGAT 0.972564 -92 ATTTAAAAGCATTTTGCGATGCAGATCGCA 5 223 0 ATTTTGCGAT 0.956703 -78 CTCTCCCTCGTTTTTTCCATACTAGATTTT 5 262 1 TTTTTTCCAT 0.920748 -39 ATTTTTTCCTTTTTATTTGAA 5 290 0 TTTTTTCCTT 0.888088 -11 ********** Masking position 5 Map Score: 7.65204 Number of sites scoring better than the average of aligned sites = 841 Number in coding regions = 686 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 3 CAAGTTGTATATTTTTTGAAACGCTGTTTTT 1 12 1 ATTTTTGAAA 0.728448 -289 CCTGTTTTTGAGTCGTTGAGTTCTACAGTCC 1 111 0 AGTGTTGAGT 0.939571 -190 GACAGTCTTAGTCTTTAAGTTGAGAAGGAT 1 281 0 AGTTTTAAGT 0.806238 -20 CTATTTGCACATTCGTTGGATCACTTCGATG 3 103 1 ATTGTTGGAT 0.912539 -78 GCTAGAGCAGATTCTTTGAATGATGTAATCT 4 37 1 ATTTTTGAAT 0.948864 -59 TATGGTTAAAAGTAGGTAAATT 4 84 1 AGTGGTAAAT 0.8062 -12 TATTAAGTTTATTAGTTAAATGTATATTTGA 5 79 0 ATTGTTAAAT 0.965488 -222 TTAGGGTTGTATTGGTTAAATATGCTAATTT 5 110 0 ATTGTTAAAT 0.965488 -191 AATAAGAAAAATTTGTTGATTAGGGTTGTAT 5 129 0 ATTGTTGATT 0.888936 -172 TTCTTATTGGATTTTTTACATTTTCAAAATA 5 152 1 ATTTTTACAT 0.736367 -149 *** ******* Masking position 7 Map Score: 4.22926 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 151 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TTTTCCTTTTGGATTAATTTCAGCGTATAA 1 44 1 GGATTAATTT 0.920792 -257 CATCCGAATGAGATTAATTTATCGCCATCG 2 42 1 AGATTAATTT 0.928026 -86 AATCTGCTCTAGCAAAATTTGACGGGATTT 4 20 0 AGCAAAATTT 0.906312 -76 AAATCCAATAAGAAAAATTTGTTGATTAGG 5 136 0 AGAAAAATTT 0.963488 -165 TTTCAAAATAAGAAAAATTTTGCAATTTTT 5 173 1 AGAAAAATTT 0.963488 -128 GGGAGAGAAACGATTAATTTAAAAGCATTT 5 239 0 CGATTAATTT 0.920792 -62 ********** Masking position 6 Map Score: 3.93554 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 57 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 TTGAGTTCTACAGTCCAAAGTGCTGAAACCAT 1 95 0 CAGCCAAGTG 0.995983 -206 GCTTGTGTCTCAGCCCAACGTGAGTGCCTGTT 1 136 0 CAGCCAAGTG 0.995983 -165 AAAAAGCGTGCAGAGGAATGTGTGCTTGTGTC 1 159 0 CAGGGAAGTG 0.984701 -142 TCTTATACGACATCCGAATGAGATTAATTTAT 2 32 1 CATCGAAGAG 0.925253 -96 TGATTCAGGTCAGGCCAAATGGCGGTATTTTA 3 47 0 CAGCCAATGG 0.908298 -134 TGAATCAATTCAGCAGGAAGTGATTGTTATAC 3 72 1 CAGAGGAGTG 0.862391 -109 TTTCATTTTGCATTCCAAAGTTCAGAGGTAGT 3 158 1 CATCCAAGTT 0.915488 -23 TTGCGATCTGCATCGCAAAATGCTTTTAAATT 5 222 1 CATGCAAATG 0.841368 -79 *** **** *** Masking position 8 Map Score: 4.46319 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 498 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 TTCGGATTTCATGTTCAAGCAACACCTGGTT 2 85 1 ATGTTCAAGA 0.961368 -43 GATCCAACGAATGTGCAAATAGTATAACAAT 3 94 0 ATGTGCAAAA 0.973148 -87 GATCACTTCGATGTGCAAGAAGACTTCCGGC 3 121 1 ATGTGCAAGA 0.967795 -60 TCTTATGCCCATTTTCAATTATGGTTAAAAG 4 65 1 ATTTTCAATA 0.882959 -31 GATTTTTTACATTTTCAAAATAAGAAAAATT 5 161 1 ATTTTCAAAT 0.751659 -140 ATGAATAAAAAATTGCAAAATTTTTCTTATT 5 179 0 AATTGCAAAT 0.721938 -122 TCCATACTAGATTTTCAAATAAAAAGGAAAA 5 277 1 ATTTTCAAAA 0.958922 -24 ********* * Masking position 7 Map Score: 2.88995 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 81 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 CAGCACTTTGGACTGTAGAACTCAACGACTCAA 1 102 1 GACTGTACTC 0.983731 -199 GACAGTCTTAGTCTTTAAGTTGA 1 288 0 GACAGTAGTC 0.976149 -13 ATAAGATTAGGACAGTGACAGTCGTTT 2 5 0 GACAGTAGTC 0.533788 -123 AGCAACACCTGGTTGTTTCAGTCAACGGAGTAT 2 102 1 GGTTGTAGTC 0.955035 -26 AGCAGGAAGTGATTGTTATACTATTTGCACATT 3 83 1 GATTGTACTA 0.93228 -98 ATAAAAAACTGGCTGTCAAACTATTTTTTGGCA 5 13 1 GGCTGTACTA 0.971125 -288 ****** **** Masking position 6 Map Score: 2.3313 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 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 8 GCACTGCCGGAAAGCGAATCCGGTATTACGAA 1 227 0 AACGAATCCG 0.943436 -74 TCCTAATCTTATACGACATCCGAATGAGATTA 2 26 1 AAGACATCCG 0.992944 -102 TGTTGCTTGAACATGAAATCCGAATGAAATAA 2 77 0 AAGAAATCCG 0.992388 -51 TCGATGTGCAAGAAGACTTCCGGCAACAGATT 3 128 1 AAGACTTCCG 0.977155 -53 TTGGAATGCAAAATGAAATCTGTTGCCGGAAG 3 144 0 AAGAAATCTG 0.96151 -37 * * ******** Masking position 9 Map Score: 1.59255 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 68 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ********** No masking Map Score: 2.12695e-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 10 ********** No masking Map Score: 2.12695e-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 11 ********** No masking Map Score: 2.12695e-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