AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_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 malP 300 maltodextrin phosphorylase #2 glgB 272 1,4-alpha-glucan branching enzyme #3 asd 192 aspartate-semialdehyde dehydrogenase #4 HI1354 300 glutaminyl-tRNA synthetase (glnS) #5 HI1355 65 conserved hypothetical protein #6 HI1356 61 4-alpha-glucanotransferase (malQ) #7 HI1358 95 glycogen operon protein (glgX) #8 HI1360 107 glycogen synthase (glgA) #9 HI1361 245 glycogen phosphorylase (glgP) Motif number 1 GCGTATTTTCAAAAAGCGGAAGGTAACTCT 1 57 0 AAAAAGCGGA 0.938903 -244 AGCCTTACCTGAAGTGAGGACGACGCAGAG 2 152 1 GAAGTGAGGA 0.897326 -121 ACATCACATTAAAAAGCGGTATCGCCGTGA 4 28 1 AAAAAGCGGT 0.96305 -273 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 4 124 0 AAAGTGCGGT 0.996527 -177 TTTAATCAACCAAGTGCGGTCAAAACAAAC 5 12 1 CAAGTGCGGT 0.983564 -54 ATACAAATAAAAAGTGCGGTCAAAATCACG 5 41 0 AAAGTGCGGT 0.996527 -25 AGCTAAGCTGAAAGTGATGACAACTGGCT 6 10 0 AAAGTGATGA 0.767549 -52 TTAGGAAAAGTGCGGTCAAAATTAAC 8 7 1 AAAGTGCGGT 0.996527 -101 GGAGGTTCAGAAAGTGCGGTTAATTTTGAC 8 25 0 AAAGTGCGGT 0.996527 -83 CCTCTTTAGCAAAGAGAGGAGTTGATCGAG 8 53 1 AAAGAGAGGA 0.961102 -55 TCACGTACTCAAAGAGCGGTCAAATTTTGA 9 141 1 AAAGAGCGGT 0.994124 -105 ********** Masking position 3 Map Score: 27.2881 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 90 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 2 TGTCACAACCAGAAGTCAAAAATCCAATTG 2 220 1 AGAAGTCAAA 0.829095 -53 GCGGACTTTCTGCGTGCTAACAAAGCAGGA 3 35 1 TGCGTGCTAA 0.866821 -158 GTGCTAACAAAGCAGGATAAGTCGCATTAC 3 48 1 AGCAGGATAA 0.803205 -145 CCATACAAAAAGCAGCCAAAGTCGCAAGTG 3 106 0 AGCAGCCAAA 0.949861 -87 CACACATCTTTGCAGGAAAAAAACGCTT 3 175 1 TGCAGGAAAA 0.940489 -18 TCGCCGTGAATGCAGGCAAAAACAGCAAAA 4 49 1 TGCAGGCAAA 0.991285 -252 ATCAACCAAGTGCGGTCAAAACAAACGTGA 5 16 1 TGCGGTCAAA 0.989917 -50 AAATAAAAAGTGCGGTCAAAATCACGTTTG 5 37 0 TGCGGTCAAA 0.989917 -29 TTATCGATTTTGTAGGCAAATTACATTTGC 7 72 0 TGTAGGCAAA 0.899621 -24 TTAGGAAAAGTGCGGTCAAAATTAACCGCA 8 11 1 TGCGGTCAAA 0.989917 -97 GTACTCAAAGAGCGGTCAAATTTTGATTGA 9 145 1 AGCGGTCAAA 0.986173 -101 ATTATTTCTTAGCATTCTAATAGAGGTTTT 9 222 1 AGCATTCTAA 0.752558 -24 ********** Masking position 9 Map Score: 17.8996 Number of sites scoring better than the average of aligned sites = 839 Number in coding regions = 769 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 3 ATCTAAGTGCAAAAAATGGCCGTTGCGTATTT 1 79 0 AAAAAGGCCG 0.968052 -222 AGCCACCCTTAAAGAATAGCCAATGCTCTATT 2 102 0 AAAGAAGCCA 0.975724 -171 CGTTCAGGTCAAAAAAATGTCACAACCAGAAG 2 203 1 AAAAATGTCA 0.915947 -70 TTCACCATACAAAAAGCAGCCAAAGTCGCAAG 3 108 0 AAAAAAGCCA 0.982058 -85 TTGTATGGTGAAAGATGTGCCAAGAGGAGACC 3 128 1 AAAGATGCCA 0.975724 -65 TGTGTGCTGTATAAATGTGCCGGTCTCCTCTT 3 149 0 ATAAATGCCG 0.901931 -44 TAAACATTCAAAAAACTTACCGCACTTTGTGC 4 116 1 AAAAATACCG 0.850686 -185 AACTTGCCATAAAAAACCGCCACGAAATTATC 4 164 0 AAAAACGCCA 0.952413 -137 AAAAGATTGTAAAAACTTGCCATAAAAAACCG 4 177 0 AAAAATGCCA 0.982058 -124 TTAGATTTGTATAGAATAGCCGAATATTTTTT 4 262 1 ATAGAAGCCG 0.871023 -39 TATCTTTGCAAAAAACAAGCCCAATCACACCG 9 66 0 AAAAAAGCCC 0.927477 -180 TCACGTACTCAAAGAGCGGTCAAATTTTGATT 9 141 1 AAAGAGGTCA 0.843372 -105 GCACGTTTGCAAAAATCAATCAAAATTTGACC 9 158 0 AAAAAAATCA 0.579615 -88 ***** ***** Masking position 5 Map Score: 15.1017 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 538 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 4 CTGCGGGGGATTAGGCAGGGAGGAGTTGCG 1 205 0 TTAGGCAGGG 0.782178 -96 TTATCGCTAGTTTGCCAGGCTCGATGTTGA 1 246 0 TTTGCCAGGC 0.881632 -55 TTTGGCTGCTTTTTGTATGGTGAAAGATGT 3 116 1 TTTTGTATGG 0.837887 -77 ATTTTGCTGTTTTTGCCTGCATTCACGGCG 4 50 0 TTTTGCCTGC 0.85057 -251 GCTGGCTGGGTTTGGTAAGCTAAACATTCA 4 96 1 TTTGGTAAGC 0.939304 -205 TTTTTATCGATTTTGTAGGCAAATTACATT 7 75 0 TTTTGTAGGC 0.971812 -21 TGAAAGAATATTTTGCAAGCGGTGTGATTG 9 47 1 TTTTGCAAGC 0.980538 -199 TGGGCTTGTTTTTTGCAAAGATAAGCATAA 9 75 1 TTTTGCAAAG 0.790701 -171 TTCGAACTACTTTTGTAGGCTGTGTAAACA 9 107 1 TTTTGTAGGC 0.971812 -139 TTTGATTGATTTTTGCAAACGTGCGTAAAT 9 166 1 TTTTGCAAAC 0.891817 -80 ********** Masking position 2 Map Score: 7.13817 Number of sites scoring better than the average of aligned sites = 973 Number in coding regions = 844 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 GGGAGGAGTTGCGGGGATGAGCAAGGAAATG 1 187 0 GCGGGATGAG 0.988864 -114 GGGGGATTAGGCAGGGAGGAGTTGCGGGGAT 1 200 0 GCGGGAGGAG 0.994301 -101 CCTAATCCCCCGCAGGATGAGGAAGGTCAAC 1 220 1 CGAGGATGAG 0.881394 -81 TGAGGACGACGCAGAGAGGATGCACAGAGTG 2 166 1 GCGAGAGGAT 0.929995 -107 TGAAAGATGTGCCAAGAGGAGACCGGCACAT 3 136 1 GCAAGAGGAG 0.990589 -57 TTTTTTTCCTGCAAAGATGTGTGCTGTATAA 3 167 0 GCAAGATGTG 0.905667 -26 GTGATGTAGTGGAGGGAGGCGTAT 4 4 0 GGGGGAGGCG 0.94251 -297 CCTCTCTTTGCTAAAGAGGAGGTTCAGAAAG 8 41 0 CTAAGAGGAG 0.806145 -67 CTTGTTTTTTGCAAAGATAAGCATAAAATTC 9 79 1 GCAAGATAAG 0.840053 -167 ** ******** Masking position 7 Map Score: 5.2386 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 393 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 CTATAAATTAAGTAAAGGAGTGAAACAGTT 1 29 0 AGTAAAGGAG 0.885037 -272 GTTAGTGCGTAATACAGGAGTAAGCGCAGA 2 48 1 AATACAGGAG 0.983613 -225 AGGGTGGCTGAATACATGAGTATTCACAGC 2 125 1 AATACATGAG 0.902781 -148 GTGACACAATAAAACAGGAAGACAAGC 2 256 1 AAAACAGGAA 0.953013 -17 AATGCAGGCAAAAACAGCAAAATTTCCTAT 4 57 1 AAAACAGCAA 0.823026 -244 TTCTATGGCAAGAACAGGAGATGAACCTTT 4 224 1 AGAACAGGAG 0.980301 -77 ********** Masking position 6 Map Score: 1.81362 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 65 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 CTATTCTTTAAGGGTGGCTGAATACATGAGTA 2 115 1 AGGGTGTGAA 0.973955 -158 GGCAATTATCAGGGAATTTGAGTT 3 3 0 AGGGAATGAG 0.925412 -190 TACAAATCTAAGGGAAAATAAAGGTTCATCTC 4 241 0 AGGGAATAAA 0.970922 -60 TCGATTTTGTAGGCAAATTACATTTGCCCAAA 7 67 0 AGGCAATACA 0.81257 -29 TTATATTTATAGGGAAAATAAAAAACTCA 8 89 1 AGGGAATAAA 0.970922 -19 CTACTTTTGTAGGCTGTGTAAACAACATTCAC 9 113 1 AGGCTGTAAA 0.92891 -133 TAATTAACGTAGGGTGTGTGAATTTTCAAAAT 9 194 0 AGGGTGTGAA 0.973955 -52 ****** **** Masking position 1 Map Score: 1.31732 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 27 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 GATTTTCTGCGCTGTATTGCATTGATTTGA 1 114 1 GCTGTATTGC 0.93658 -187 TTTCAACACAACGTTATCGCTAGTTTGCCA 1 259 0 ACGTTATCGC 0.898941 -42 ACTAACAGGGGCGGCATCGCGCCCCAGATT 2 24 0 GCGGCATCGC 0.92743 -249 ACATTAAAAAGCGGTATCGCCGTGAATGCA 4 33 1 GCGGTATCGC 0.657946 -268 ********** Masking position 6 Map Score: 0.808109 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 348 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 AACCACAGGATTAGCATCAAATCAATGCAAT 1 129 0 TTGCATCAAA 0.870595 -172 TTGTAAAAACTTGCCATAAAAAACCGCCACG 4 172 0 TTCCATAAAA 0.931627 -129 AAATACTAGATTTAAATAAAAGATTGTAAAA 4 195 0 TTAAATAAAA 0.864791 -106 TCTCCTGTTCTTGCCATAGAAATACTAGATT 4 214 0 TTCCATAGAA 0.854203 -87 TTCCCTTAGATTTGTATAGAATAGCCGAATA 4 257 1 TTGTATAGAA 0.681977 -44 TTTCTCTCGTTAAAATAAAAAAATATTCGG 4 281 0 TTAAATAAAA 0.865292 -20 AGTTGATACAAATAAAAAGTGCGGTCA 5 49 0 TAAAATAAAA 0.744178 -17 TAAGAAAGTTTACGAATAAAA 9 1 0 TAGAATAAAA 0.881504 -245 TATGCTTATCTTTGCAAAAAACAAGCCCAAT 9 73 0 TTGCAAAAAA 0.819584 -173 TTTGCAAAGATAAGCATAAAATTCGAACTAC 9 86 1 TAGCATAAAA 0.935986 -160 ** ******** Masking position 6 Map Score: 1.88577 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 148 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 10 ATACAGATTTTCTGCGCTGTATTGCATTGA 1 109 1 TCTGCGCTGT 0.94895 -192 TCATGAAACATCTGCGCTTACTCCTGTATT 2 58 0 TCTGCGCTTA 0.910012 -215 GTGCATCCTCTCTGCGTCGTCCTCACTTCA 2 161 0 TCTGCGTCGT 0.979184 -112 TGCACAGAGTGCTGCGCCGTTCAGGTCAAA 2 186 1 GCTGCGCCGT 0.98082 -87 ********** Masking position 3 Map Score: 0.257307 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 338 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ATACGCCTCCCTCCACTACATCACATTAAA 4 11 1 CTCCACTACA 0.960812 -290 ATTTATACATCGCCACGATAATTTCGTGGC 4 148 1 CGCCACGATA 0.982219 -153 CATAAAAAACCGCCACGAAATTATCGTGGC 4 159 0 CGCCACGAAA 0.982218 -142 GAATGTAATTCGCCCCTACAATTTATCTAT 7 16 0 CGCCCCTACA 0.9828 -80 ********** Masking position 8 Map Score: 0.180806 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 90 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 CTTCAGGTAAGGCTGTGAATACTCATGTAT 2 136 0 GGCTGTGAAT 0.95871 -137 CGGCGCAGCACTCTGTGCATCCTCTCTGCG 2 175 0 CTCTGTGCAT 0.930624 -98 AAAGCGGTATCGCCGTGAATGCAGGCAAAA 4 40 1 CGCCGTGAAT 0.95791 -261 ACTTACCGCACTTTGTGCATTTATACATCG 4 130 1 CTTTGTGCAT 0.771492 -171 ATTTTGCAAGCGGTGTGATTGGGCTTGTTT 9 56 1 CGGTGTGATT 0.80624 -190 CGCTCTTTGAGTACGTGAATGTTGTTTACA 9 129 0 GTACGTGAAT 0.853889 -117 TTTTGCAAACGTGCGTAAATTTTGAAAATT 9 176 1 GTGCGTAAAT 0.721667 -70 TTAACGTAGGGTGTGTGAATTTTCAAAATT 9 193 0 GTGTGTGAAT 0.959495 -53 ********** Masking position 6 Map Score: 0.674374 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 220 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ********** No masking Map Score: -2.68342e-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: -2.68342e-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: -2.68342e-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