AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i092_Sugar_Utilization_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 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #2 bglG 285 positive regulation of bgl operon Motif number 1 GCAATTTTTTTCAGGTTTTGCCCGCTTAGT 1 43 0 TCAGGTTTTG 0.99411 -91 GCCGTTTTTTTCAGGTTTTTTTTTGGAGTT 1 87 1 TCAGGTTTTT 0.988493 -47 CAGGTTTTTTTTTGGAGTTTTGCCGCAAAG 1 98 1 TTTGGAGTTT 0.834769 -36 AATTAAGTTATTGGGATTTGTCTGGTGAA 2 10 0 TTGGGATTTG 0.988263 -276 AACTTAATTATTGGGATTTGTTATATATAA 2 31 1 TTGGGATTTG 0.988263 -255 TTGTGTAATTTTAGGAATTTATAAAGTTAT 2 57 0 TTAGGAATTT 0.86413 -229 TCTGGTTATGTCAGGTTTTGCCTGCGAATG 2 218 0 TCAGGTTTTG 0.99411 -68 ACCAGTATTCTCTGGTTATGTCAGGTTTTG 2 228 0 TCTGGTTATG 0.934469 -58 ACTGGTGAAGTCGGGTTTTTTTGTTTATAA 2 252 1 TCGGGTTTTT 0.990452 -34 ********** Masking position 9 Map Score: 17.687 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 416 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 AATATTATTACTGAGTAAAGGATT 1 5 1 TTATTACTGA 0.895816 -129 GAGTAAAGGATTGTTACCGCACTAAGCGGG 1 23 1 TTGTTACCGC 0.842485 -111 ATCAAGCAATTTTTTTCAGGTTTTGCCCGC 1 48 0 TTTTTTCAGG 0.96106 -86 GTCAGGCCGTTTTTTTCAGGTTTTTTTTTG 1 82 1 TTTTTTCAGG 0.96106 -52 TTTTTCAGGTTTTTTTTTGGAGTTTTGCCG 1 93 1 TTTTTTTTGG 0.904523 -41 CCCAATAACTTAATTATTGGGATTTGTTAT 2 25 1 TAATTATTGG 0.849585 -261 TAACTTTGTGTAATTTTAGGAATTTATAAA 2 62 0 TAATTTTAGG 0.794155 -224 TACACAAAGTTAATAACTGCGAGCATGGTC 2 80 1 TAATAACTGC 0.64841 -206 CGCATTGCTATTTTCTCTGCACGCAATTAA 2 126 1 TTTTCTCTGC 0.894036 -160 GCAATTAAATTAATTTCCGAACCTGGATGT 2 148 1 TAATTTCCGA 0.735256 -138 ATCCAGTCATTTATTAATGGTTTTTATAAC 2 180 0 TTATTAATGG 0.796716 -106 AATGACTGGATTGTTACTGCATTCGCAGGC 2 199 1 TTGTTACTGC 0.92559 -87 TATTCTCTGGTTATGTCAGGTTTTGCCTGC 2 223 0 TTATGTCAGG 0.864835 -63 ACTTCACCAGTATTCTCTGGTTATGTCAGG 2 233 0 TATTCTCTGG 0.903903 -53 ********** Masking position 4 Map Score: 12.3496 Number of sites scoring better than the average of aligned sites = 3221 Number in coding regions = 2759 Number in noncoding regions = 462 Number of orfs with sites within 600 bp upstream = 456 Fraction of orfs with sites within 600 bp upstream = 0.0732412 Motif number 3 TTTGCCCGCTTAGTGCGGTAACAATCCTTT 1 27 0 TAGTGCGGTA 0.91559 -107 AGTTTTGCCGCAAAGCGGTAGAGGGCAAGT 1 113 1 CAAAGCGGTA 0.990223 -21 GAGAAAATAGCAATGCGCTATTGATAAAAA 2 113 0 CAATGCGCTA 0.984297 -173 TTTTGCCTGCGAATGCAGTAACAATCCAGT 2 203 0 GAATGCAGTA 0.963572 -83 ********** Masking position 2 Map Score: 1.74914 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 189 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 CGGGCAAAACCTGAAAAAAATTGCTTGATT 1 49 1 CTGAAAAAAA 0.946752 -85 AAAAAAAAACCTGAAAAAAACGGCCTGACG 1 81 0 CTGAAAAAAA 0.946752 -53 AATTTATAAAGTTATATATAACAAATCCCA 2 42 0 GTTATATATA 0.743669 -244 TATATATAACTTTATAAATTCCTAAAATTA 2 52 1 TTTATAAATT 0.738292 -234 CAATGCGCTATTGATAAAAATATGACCATG 2 103 0 TTGATAAAAA 0.963133 -183 CTGGATGTTCGTTATAAAAACCATTAATAA 2 170 1 GTTATAAAAA 0.958489 -116 GGTTTTTTTGTTTATAAAAAAGGTCCTTGC 2 265 1 TTTATAAAAA 0.797672 -21 ********** Masking position 6 Map Score: 4.81419 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 261 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 ACCTGAAAAAAATTGCTTGATTCACGTCAG 1 57 1 AATTGCTTGA 0.959048 -77 ACCTGAAAAAAACGGCCTGACGTGAATCAA 1 73 0 AACGGCCTGA 0.968792 -61 CAAAGTTAATAACTGCGAGCATGGTCATAT 2 84 1 AACTGCGAGC 0.979263 -202 AAATTAATTTAATTGCGTGCAGAGAAAATA 2 134 0 AATTGCGTGC 0.9931 -152 TTATGTCAGGTTTTGCCTGCGAATGCAGTA 2 213 0 TTTTGCCTGC 0.930039 -73 ********** Masking position 5 Map Score: 1.44057 Number of sites scoring better than the average of aligned sites = 1031 Number in coding regions = 938 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 ATAATTAAGTTATTGGGATTTGTCTGGTGA 2 12 0 TATTGGGATT 0.990577 -274 ATAACTTAATTATTGGGATTTGTTATATAT 2 29 1 TATTGGGATT 0.990577 -257 ATCAATAGCGCATTGCTATTTTCTCTGCAC 2 118 1 CATTGCTATT 0.935912 -168 AGTCATTTATTAATGGTTTTTATAACGAAC 2 176 0 TAATGGTTTT 0.914743 -110 ********** Masking position 4 Map Score: 1.07838 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 67 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 ********** No masking Map Score: -2.7468e-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: -2.7468e-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: -2.7468e-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