AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i038_Galactose_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 galE 260 UDP-galactose-4-epimerase #2 HI0351 172 UDP-glucose 4-epimerase (galE) #3 HI0819 37 galactokinase (galK) #4 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) Motif number 1 GATTGCGCTTTTTATCTGAAAAAAGACGCGGTTT 1 84 0 TTTATAAAAA 0.936062 -177 TTAGCCGTTTTTTATGCGCGATTAAGTGATTATA 1 137 0 TTTATCGATA 0.949536 -124 GGTTTTTTATTTTATTGAAAATCACCATTCTTAC 2 95 1 TTTATAAATA 0.974564 -78 GATATAATTTTTTAGTCTCAATAATTAACAAGGA 2 142 1 TTTAGCAATA 0.984532 -31 TCGTAAATTATTTATGATCAAAATATAAGATTTA 4 34 0 TTTATCAAAT 0.90985 -174 CCGCTTTCAATTTATCGTAAATTATTTATGATCA 4 48 0 TTTATAAATA 0.974683 -160 TATTTTCTTATTTTGTGACAAAGATCACGGTTTA 4 123 1 TTTTGCAAAA 0.885689 -85 AAGATCACGGTTTATTTACAATAATTTAGTATAA 4 143 1 TTTATCAATA 0.984744 -65 TTTACAATAATTTAGTATAAATTAATGTAATCGT 4 157 1 TTTAGAAATA 0.964812 -51 TTGACTCCTGTTTTTTATCAATGTAAACGATTAC 4 183 0 TTTTTCAATT 0.874471 -25 ***** **** * Masking position 11 Map Score: 11.2176 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 182 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 GAATGATTGCGCTTTTTATCTGAAAAAAGA 1 92 0 GCTTTTTATC 0.973678 -169 GAATTTAGCCGTTTTTTATGCGCGATTAAG 1 145 0 GTTTTTTATG 0.984932 -116 CTACAACAATACTTTTTAGCAACAGGTTTT 2 71 1 ACTTTTTAGC 0.929569 -102 TTAGCAACAGGTTTTTTATTTTATTGAAAA 2 86 1 GTTTTTTATT 0.966678 -87 TAGTGATATAATTTTTTAGTCTCAATAATT 2 138 1 ATTTTTTAGT 0.911946 -35 TTTATCGTAAATTATTTATGATCAAAATAT 4 42 0 ATTATTTATG 0.880741 -166 AATAAGCAAAATTTTTTATGATTTAGTTCA 4 97 0 ATTTTTTATG 0.976309 -111 TTTGACTCCTGTTTTTTATCAATGTAAACG 4 188 0 GTTTTTTATC 0.984931 -20 ********** Masking position 8 Map Score: 10.4642 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 153 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 3 CTCTCCGGCCAACGGTTCGACGCATGCAGGCA 1 50 1 AACGGTTGCG 0.90554 -211 TGAAAAAAGACGCGGTTTCATGCCTGCATGCG 1 70 0 CGCGGTTCTG 0.968926 -191 AGGGTTTATGAATGATTGCGCTTTTTATCTGA 1 99 0 AATGATTCCT 0.881529 -162 GTTTTTTATGCGCGATTAAGTGATTATAAAAC 1 133 0 CGCGATTATG 0.879631 -128 GCGCATAAAAAACGGCTAAATTCTTGTGTAAA 1 152 1 AACGGCTATT 0.870702 -109 TTCTTGTGTAAACGATTCCACTAATTTATTCC 1 172 1 AACGATTCCT 0.966186 -89 AATGATTTCCTTGTTAATTATT 2 161 0 AATGATTCTT 0.913084 -12 ATAAATTGAAAGCGGTTACTTTCATAAGTATG 4 67 1 AGCGGTTCTT 0.985887 -141 TGACAAAGATCACGGTTTATTTACAATAATTT 4 138 1 CACGGTTATT 0.958303 -70 TATCAATGTAAACGATTACATTAATTTATACT 4 170 0 AACGATTCTT 0.98346 -38 ******* * ** Masking position 7 Map Score: 7.80037 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 869 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 GATGCGAAAAGTGTGACATGGAATAAATTAG 1 192 0 GTGTGAATGG 0.95234 -69 TAGGCTTATGGTATGAAATAACCATAGCATA 1 228 0 GTATGAATAA 0.964519 -33 TCCATTAGTTGTGTGATATAAGGTTAT 2 7 0 GTGTGAATAA 0.98817 -166 TTGTTGTAGCGAGTGAGATAACCTCTCATAT 2 49 0 GAGTGAATAA 0.963542 -124 TCACTATTTTGTGTGGTAAGAATGGTGATTT 2 113 0 GTGTGGAAGA 0.833624 -60 CCACACAAAATAGTGATATAATTTTTTAGTC 2 128 1 TAGTGAATAA 0.896489 -45 CGTAAATTATTTATGATCAAAATATAAGATT 4 36 0 TTATGACAAA 0.697274 -172 ACTTTCATAAGTATGAACTAAATCATAAAAA 4 84 1 GTATGACTAA 0.930539 -124 TTTTCTTATTTTGTGACAAAGATCACGGTTT 4 125 1 TTGTGAAAAG 0.875316 -83 ****** **** Masking position 4 Map Score: 6.7751 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 194 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 TAACCATAGCATAACAAAGATGCGAAAAGT 1 211 0 ATAACAAAGA 0.980849 -50 GTCTCAATAATTAACAAGGAAATCATT 2 156 1 TTAACAAGGA 0.982234 -17 CTCTTTAGCTTTAGCAAAGAGGG 3 25 1 TTAGCAAAGA 0.958458 -13 TTTATAGATTATAACAAGGAAAAAGTT 4 8 0 ATAACAAGGA 0.982234 -200 TTCTTATTTTGTGACAAAGATCACGGTTTA 4 127 1 GTGACAAAGA 0.950961 -81 ********** Masking position 6 Map Score: 4.51257 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 38 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 AATTAGTGGAATCGTTTACACAAGAATTTA 1 168 0 ATCGTTTACA 0.98658 -93 TATGAAAGTAACCGCTTTCAATTTATCGTA 4 63 0 ACCGCTTTCA 0.961969 -145 ATAAACCGTGATCTTTGTCACAAAATAAGA 4 128 0 ATCTTTGTCA 0.915636 -80 AATTAATGTAATCGTTTACATTGATAAAAA 4 176 1 ATCGTTTACA 0.98658 -32 ********** Masking position 6 Map Score: 0.0547533 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 144 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ********** No masking Map Score: -1.46782e-13 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 8 ********** No masking Map Score: -1.46782e-13 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: -1.46782e-13 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