AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i035_Sugars_Metabolism_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 BIME6 21 BIME #2 araB 300 L-ribulokinase #3 yiaM 117 orf, hypothetical protein #4 sgaT 291 orf, hypothetical protein #5 HI1024 49 hexulose-6-phosphate synthase, putative #6 HI1027 58 L-xylulose kinase (lyx) #7 HI1028 30 conserved hypothetical protein #8 HI1030 71 conserved hypothetical transmembrane protein #9 HI1031 175 conserved hypothetical protein Motif number 1 TATGACAGACATAGCCTCAAGGAATAGCT 3 99 1 ATACCTAAAA 0.827675 -19 AGTGTCAGGATTAATCAAAACCAATCACATATTG 4 38 0 TTATCAAAAA 0.945264 -254 AAATCTTTCCATACTCAAAATCAACAACAACTTC 4 116 0 ATATCAAAAA 0.959765 -176 GTGTAATTCAATTAACTAAATGAATTTAAATGGA 4 158 1 ATTACTAAAA 0.917832 -134 ATAGAGTGGGATTCACACAACGAAACAATTATCC 4 189 0 ATTACAAAAA 0.969153 -103 CGCGTCACATTTAATCATAAATAATCTTGTTGTG 4 245 1 TTATCAAAAA 0.938543 -47 TCACTCTAATTTTCAAAAGTAATCACAACAAG 4 270 0 ATTTCAAAAA 0.978657 -22 CGTTTTTCCTTAAATAATATGAGGAAG 5 33 0 TTTCCTAAAA 0.870419 -17 ATAGGCTGGATTTTACATAATAAAAATCCAGCCC 6 14 1 TTTACAAAAA 0.957678 -45 ACGAATCACATTTGTGATAATCAATTGGAGGTGT 8 47 1 TTTTGAAAAA 0.779962 -25 AATATGAAATATTATCACAAGAAAATAGGATCTA 9 16 1 ATTTCAAAAA 0.978711 -160 ACGTTTCATAATTTACAAAAATAAGAAAGCTCAG 9 120 0 ATTACAAAAA 0.969152 -56 *** *** ** ** Masking position 9 Map Score: 15.3747 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 144 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 GTCCATATTGCATCAGACATTG 2 3 1 CCATATTGCA 0.94772 -298 GCAGAAAAGTCCACATTGATTATTTGCACG 2 161 1 CCACATTGAT 0.980205 -140 GCACGGCGTCACACTTTGCTATGCCATAGC 2 186 1 ACACTTTGCT 0.934896 -115 AAAACCAATCACATATTGATTCGAATTGAA 4 26 0 ACATATTGAT 0.969559 -266 TAATTGAATTACACATTCCATTAAATCTTT 4 142 0 ACACATTCCA 0.829211 -150 GCAAATAATTCCACATGGATAGAGTGGGAT 4 211 0 CCACATGGAT 0.929339 -81 TTTACTGGAAACATATTGCTG 8 2 0 ACATATTGCT 0.98059 -70 AATTATTTTAACATATTGATTTATAAATAA 9 67 1 ACATATTGAT 0.969559 -109 ********** Masking position 3 Map Score: 8.24877 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 197 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 GACACTTTTGTTACGCGTTTTTGTCATGGCT 2 120 0 TTACCGTTTT 0.871942 -181 CCGTGATTATAGACACTTTTGTTACGCGTTT 2 131 0 AGACCTTTTG 0.77232 -170 GGATCCTACCTGACGCTTTTTATCGCAACTC 2 237 1 TGACCTTTTT 0.978928 -64 CTGTTTCTCCATACCCGTTTTTTTGGATGGA 2 272 1 ATACCGTTTT 0.75916 -29 GTTCTGGCGTAGACGATTATTCGA 3 4 0 AGACATTATT 0.586231 -114 AATCACATATTGATTCGAATTGAACTATCAT 4 19 0 TGATCGAATT 0.732406 -273 AATCAATATGTGATTGGTTTTGATTAATCCT 4 35 1 TGATGGTTTT 0.807911 -257 TGATTAATCCTGACACTATTTTTTCAGGAAG 4 55 1 TGACCTATTT 0.955568 -237 AGGAAGGCAATGACCATTTTTTGACTTTTTG 4 80 1 TGACATTTTT 0.937438 -212 AATCTTGTTGTGATTACTTTTGAAAATTAGA 4 267 1 TGATACTTTT 0.681604 -25 ATCACAAATGTGATTCGTTTTATATTATGGC 8 34 0 TGATCGTTTT 0.966607 -38 TATTTTCTTGTGATAATATTTCATATTGTGA 9 12 0 TGATATATTT 0.788638 -164 TTTGTGATCTAGATCCTATTTTCTTGTGATA 9 28 0 AGATCTATTT 0.842355 -148 **** ****** Masking position 3 Map Score: 7.3916 Number of sites scoring better than the average of aligned sites = 1056 Number in coding regions = 868 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 4 CACTGCGTCTTTTACTGGCTCTTCTCGCTA 2 37 1 TTTACTGGCT 0.966796 -264 CCATACCCGTTTTTTTGGATGGAGTGAAAC 2 280 1 TTTTTTGGAT 0.871847 -21 GCAATGACCATTTTTTGACTTTTTGCCAGG 4 86 1 TTTTTTGACT 0.794883 -206 TATGGAAAGATTTAATGGAATGTGTAATTC 4 137 1 TTTAATGGAA 0.871865 -155 ATTCATTTAGTTAATTGAATTACACATTCC 4 153 0 TTAATTGAAT 0.781512 -139 CTAAATGAATTTAAATGGATAATTGTTTCG 4 173 1 TTAAATGGAT 0.809189 -119 CCTCATATTATTTAAGGAAAAACG 5 36 1 TTTAAGGAAA 0.576901 -14 TCCTTAGTTTTTTATGGGCTGGATTTTTAT 6 33 0 TTTATGGGCT 0.919362 -26 ATTATGGCGTTTTACTGGAAACATATTGCT 8 12 0 TTTACTGGAA 0.914542 -60 TTAAAATAATTTTACTGATTTTGTGATCTA 9 48 0 TTTACTGATT 0.745776 -128 TTATTTTACATTTATTGACTGAGCTTTCTT 9 102 1 TTTATTGACT 0.939826 -74 ********** Masking position 2 Map Score: 4.86928 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 662 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 5 CAAAAGTGTCTATAATCACGGCAGAAAAGT 2 141 1 TATAATCACG 0.898818 -160 TAACTATATTAATAATTCAGGTTGCTGCAC 3 56 1 AATAATTCAG 0.888538 -62 AGGAAGGCAGTATAATTCTGTCTTTAAT 5 9 0 TATAATTCTG 0.847473 -41 TTTTATTATGTAAAATCCAGCCTATTGA 6 9 0 TAAAATCCAG 0.966463 -50 TTTACATAATAAAAATCCAGCCCATAAAAA 6 25 1 AAAAATCCAG 0.926127 -34 TTTTATATAGTAAAATTACGTTTCATAATT 9 141 0 TAAAATTACG 0.905459 -35 TTTTACTATATAAAATTAAGAGAGGAAAAA 9 156 1 TAAAATTAAG 0.920332 -20 ********** Masking position 5 Map Score: 2.9535 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 164 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 TTACATACCGGATGCGGCTAC 1 7 0 TACCGGATGC 0.974958 -15 TAAGCGGGGTTACCGGTTGGGTTAGCGAGA 2 59 0 TACCGGTTGG 0.974958 -242 CCCGCTTTGTTACAGAATGCTTTTAATAAG 2 85 0 TACAGAATGC 0.879008 -216 GATAAAAAGCGTCAGGTAGGATCCGCTAAT 2 231 0 GTCAGGTAGG 0.901991 -70 ATATTAATAATTCAGGTTGCTGCACATGCG 3 61 1 TTCAGGTTGC 0.97915 -57 ACACTATTTTTTCAGGAAGGCAATGACCAT 4 67 1 TTCAGGAAGG 0.961788 -225 ********** Masking position 5 Map Score: 1.8791 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 358 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 AACTATATTAATAATTCAGGTTGCTGCACA 3 57 1 ATAATTCAGG 0.891163 -61 TATGTCTGTCATAATTCAAGTCGCATGTGC 3 82 0 ATAATTCAAG 0.963781 -36 TACCTTCATGATAGTTCAATTCGAATCAAT 4 12 1 ATAGTTCAAT 0.923627 -280 AATGGAATGTGTAATTCAATTAACTAAATG 4 150 1 GTAATTCAAT 0.924058 -142 AAGATTATTTATGATTAAATGTGACGCGAC 4 243 0 ATGATTAAAT 0.768485 -49 TAAATTATTTATAAATCAATATGTTAAAAT 9 71 0 ATAAATCAAT 0.944684 -105 TAAATGTAAAATAAATAAATTATTTATAAA 9 86 0 ATAAATAAAT 0.824293 -90 ********** Masking position 8 Map Score: 1.18017 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 64 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 ********** No masking Map Score: -1.17707e-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 9 ********** No masking Map Score: -1.17707e-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: -1.17707e-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