AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i092_Sugar_Utilization_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 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #2 bglG 285 positive regulation of bgl operon #3 BIME185 97 BIME #4 pstC 86 high-affinity phosphate-specific transport system, cytoplasmic membrane component #5 pstS 300 high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein Motif number 1 TTAGTGCGGTAACAATCCTTTACTCAGTAATA 1 16 0 AACAATCTTA 0.895397 -118 GCACTAAGCGGGCAAAACCTGAAAAAAATTGC 1 41 1 GGCAAACCTA 0.987994 -93 AAAACTCCAAAAAAAAACCTGAAAAAAACGGC 1 87 0 AAAAAACCTA 0.909925 -47 ACCGCTTTGCGGCAAAACTCCAAAAAAAAACC 1 100 0 GGCAAACTCA 0.973114 -34 TTCACCAGACAAATCCCAATAACTTAATT 2 8 1 GACAAACCCA 0.991603 -278 AGTTATATATAACAAATCCCAATAATTAAGTT 2 31 0 AACAAACCCA 0.988763 -255 CAGAGAAAATAGCAATGCGCTATTGATAAAAA 2 113 0 AGCAATCGCA 0.920616 -173 TGCATTCGCAGGCAAAACCTGACATAACCAGA 2 216 1 GGCAAACCTA 0.987994 -70 TTTTATAAACAAAAAAACCCGACTTCACCAGT 2 252 0 AAAAAACCCA 0.931302 -34 AACTCCATGTGACAAACCGTCATCTTCGGCTA 5 64 1 GACAAACGTA 0.968879 -237 GTAGCCAACAAACAATGCTTTATGAATCCTCC 5 268 1 AACAATCTTA 0.895397 -33 ****** *** * Masking position 5 Map Score: 16.4032 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 409 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 AATATTATTACTGAGTAAAGGATTGTTAC 1 10 1 ACTGAGTAAA 0.838321 -124 GCGGGCAAAACCTGAAAAAAATTGCTTGAT 1 48 1 CCTGAAAAAA 0.927655 -86 CAAAAAAAAACCTGAAAAAAACGGCCTGAC 1 82 0 CCTGAAAAAA 0.927655 -52 CGGCAAAACTCCAAAAAAAAACCTGAAAAA 1 93 0 CCAAAAAAAA 0.727303 -41 TTCACCAGACAAATCCCAATAACT 2 5 1 CCAGACAAAT 0.878951 -281 TTAATTGCGTGCAGAGAAAATAGCAATGCG 2 126 0 GCAGAGAAAA 0.967311 -160 TACTGCATTCGCAGGCAAAACCTGACATAA 2 213 1 GCAGGCAAAA 0.752405 -73 CCTGACATAACCAGAGAATACTGGTGAAGT 2 233 1 CCAGAGAATA 0.873451 -53 TTAACCGTGTACAGAGTCAAAAAGGCGCTC 3 73 0 ACAGAGTCAA 0.769398 -25 TAAAAACATAACAGGAAGAAAAATGCCCCG 5 19 0 ACAGGAAGAA 0.847149 -282 TCATTCTGTGACAGAGAAAAAGTAGCCGAA 5 88 0 ACAGAGAAAA 0.98375 -213 TTTCTCTGTCACAGAATGAAAATTTTTCTG 5 99 1 ACAGAATGAA 0.848211 -202 CGAAGAGATGACAGAAAAATTTTCATTCTG 5 110 0 ACAGAAAAAT 0.917146 -191 CAGTTTTATGACAGAGAGATAAAGTCTTCA 5 189 0 ACAGAGAGAT 0.899437 -112 ********** Masking position 2 Map Score: 12.8294 Number of sites scoring better than the average of aligned sites = 1388 Number in coding regions = 1149 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 3 AACTTGCCCTCTACCGCTTTGCGGC 1 119 0 GCCCTCTACC 0.937458 -15 ACACGGTTTTCCCCTCACCCTAACCCTCTC 3 19 1 CCCCTCACCC 0.997077 -79 CCTCACCCTAACCCTCTCCCCAGAGGGGCG 3 31 1 ACCCTCTCCC 0.981405 -67 CTCGGTCGGTCCCCTCGCCCCTCTGGGGAG 3 46 0 CCCCTCGCCC 0.995027 -52 CGGCGTAAAACACCGTACCCGGCCTGGAGT 4 15 0 CACCGTACCC 0.892089 -72 CGGTGTTTTACGCCGCATCCGGCATTACAA 4 30 1 CGCCGCATCC 0.969612 -57 AAGAAAAATGCCCCGCTTACGCA 5 4 0 CCCCGCTTAC 0.947525 -297 ********** Masking position 4 Map Score: 6.49006 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 421 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 CGTGAATCAAGCAATTTTTTTCAGGTTTTGCC 1 51 0 GCATTTTTTC 0.83224 -83 ATTCACGTCAGGCCGTTTTTTTCAGGTTTTTT 1 76 1 GGCTTTTTTT 0.978486 -58 CTGCGAGCATGGTCATATTTTTATCAATAGCG 2 96 1 GGCTATTTTT 0.864855 -190 ATAGCGCATTGCTATTTTCTCTGCACGCAATT 2 122 1 GCATTTCTCT 0.860764 -164 TGGTGAAGTCGGGTTTTTTTGTTTATAAAAAA 2 254 1 GGTTTTTTGT 0.853655 -32 AGCAAGGACCTTTTTTATAAACAAAAA 2 269 0 GGCTTTTTTA 0.934948 -17 GACCGACCGAGCGCCTTTTTGACTCTGTACAC 3 65 1 GCCTTTTTGA 0.905833 -33 TGCGTAAGCGGGGCATTTTTCTTCCTGTTATG 5 11 1 GGCTTTTTCT 0.986327 -290 GTCATCTTCGGCTACTTTTTCTCTGTCACAGA 5 82 1 GCATTTTTCT 0.967366 -219 GTCACAGAATGAAAATTTTTCTGTCATCTCTT 5 106 1 GAATTTTTCT 0.849895 -195 ** * ******* Masking position 6 Map Score: 5.72698 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 434 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 5 TATATATAACTTTATAAATTCCTAAAATTACA 2 52 1 TTTATAATCC 0.946336 -234 TTACACAAAGTTAATAACTGCGAGCATGGTCA 2 79 1 TTAATAATCG 0.902446 -207 ATTAATGGTTTTTATAACGAACATCCAGGTTC 2 166 0 TTTATAAGAC 0.942992 -120 ATAAAAACCATTAATAAATGACTGGATTGTTA 2 183 1 TTAATAATAC 0.877827 -103 AAGGACCTTTTTTATAAACAAAAAAACCCGAC 2 261 0 TTTATAACAA 0.683511 -25 ACAAAGTCATTTTGTAATGCCGGATGCGGCGT 4 39 0 TTTGTAAGCG 0.946138 -48 ACAAAATGACTTTGTAAACGCGTTTAACTGAA 4 56 1 TTTGTAACCG 0.923426 -31 ATTACAAACATTAATAACGAAGAGATGACAGA 5 125 0 TTAATAAGAG 0.896662 -176 GTTATTAATGTTTGTAATTGACTGAATATCAA 5 139 1 TTTGTAATAC 0.918689 -162 ******* * ** Masking position 6 Map Score: 2.92131 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 166 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 AATATTATTACTGAGTAAAGGATTGT 1 6 1 TATTACTGGT 0.71404 -128 GACAAATCCCAATAACTTAATTATTGGGATT 2 18 1 AATAACTTAT 0.913155 -268 ATTTGTTATATATAACTTTATAAATTCCTAA 2 46 1 TATAACTTAT 0.866834 -240 GCTCGCAGTTATTAACTTTGTGTAATTTTAG 2 73 0 ATTAACTTGT 0.927893 -213 AGGTTCGGAAATTAATTTAATTGCGTGCAGA 2 141 0 ATTAATTTAT 0.428724 -145 ACCATTAATAAATGACTGGATTGTTACTGCA 2 189 1 AATGACTGAT 0.950715 -97 CGAGCGCCTTTTTGACTCTGTACACGGTTAA 3 72 1 TTTGACTCGT 0.797789 -26 GGCATTACAAAATGACTTTGTAAACGCGTTT 4 50 1 AATGACTTGT 0.962028 -37 AATGTTTGTAATTGACTGAATATCAACGCTT 5 145 1 ATTGACTGAT 0.934275 -156 ******** ** Masking position 5 Map Score: 2.55497 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 222 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 GCGCTCGGTCGGTCCCCTCGCCCCTCTGGG 3 49 0 GGTCCCCTCG 0.972981 -49 GATGACGGTTTGTCACATGGAGTTGGCAGG 5 58 0 TGTCACATGG 0.974385 -243 AAAATTTTTCTGTCATCTCTTCGTTATTAA 5 117 1 TGTCATCTCT 0.920573 -184 TACATATAACTGTCACCTGTTTGTCCTATT 5 229 1 TGTCACCTGT 0.988777 -72 AATGTCTCCTGGGAGGATTCAT 5 289 0 TGTCTCCTGG 0.987431 -12 ********** Masking position 3 Map Score: 1.64141 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 209 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 8 ********** No masking Map Score: 6.2771e-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: 6.2771e-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 10 ********** No masking Map Score: 6.2771e-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