AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_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 ycaI 129 orf, hypothetical protein #2 msbA 36 ATP-binding transport protein; multicopy suppressor of htrB #3 ycaQ 36 orf, hypothetical protein #4 ycaR 51 orf, hypothetical protein #5 b2253 274 putative enzyme #6 HI0058 70 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) #7 HI0059 72 conserved hypothetical protein #8 HI0060 40 ABC transporter, ATP-binding protein (msbA) #9 HI0061 258 recombination protein (rec2) #10 HI1279 104 acylneuraminate cytidylyltransferase (neuA) Motif number 1 GGAAGCTGCCTCGCAGAGTTTTGAACAGTTT 1 82 1 TCGAGAGTTT 0.897975 -48 ATTCAGAAGAATTTAACGAAAGGG 1 116 0 CAGAGAATTT 0.894424 -14 TTTGCCGACATCGTAGGATTTTTAATATTAC 5 92 0 TCGAGGATTT 0.796295 -183 CGGCAAAATGCCTCAAAATTTTGCCAAATGC 5 116 1 CCTAAAATTT 0.90034 -159 TAAGAAAAAATATAAAAATTTCAATATTTAC 5 157 1 TATAAAATTT 0.886257 -118 AATATTCTATCCTTAAAATTTCGCTCCAAAT 5 217 1 CCTAAAATTT 0.90034 -58 CCGCACTTATTAGAAAGGATTTTCT 7 58 1 TAGAAGGATT 0.776903 -15 CGCTATCTAATAGTAAAAATTGCACGCATTG 8 17 0 TAGAAAAATT 0.955477 -24 TTTATACCGCCCGCAAAAATTGGGTTCCTAA 9 94 0 CCGAAAAATT 0.961364 -165 ATAAATTTTTCAGGAAAATTTACTTGCTAAA 9 142 0 CAGAAAATTT 0.952465 -117 GCGATCCATATCGTAAAAATAAATTTTTCAG 9 160 0 TCGAAAAATA 0.734984 -99 ACGATATGGATCGCAAAATTTGAAGCAACCG 9 177 1 TCGAAAATTT 0.971783 -82 TTTTATAAAAGATTAATTCCAGCC 9 245 0 TATAAAGATT 0.805559 -14 TGTGGTGCCATATTAAAGATTAGTTTTTGCT 10 37 1 TATAAAGATT 0.805559 -68 TCCCTTGTTTTAGCAAAAACTAATCTTTAAT 10 48 0 TAGAAAAACT 0.74436 -57 *** ******* Masking position 5 Map Score: 13.6171 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 530 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 2 ACTTGAACGAGAGAAAAGCACCTGTCGGGTG 1 24 1 GAAAAAGCAC 0.99226 -106 TTAGAGAAATGAAAAAAGCACCCGACAGGTG 1 42 0 GAAAAAGCAC 0.992262 -88 ACTCCACCTATAGACAAGCGCAACCAGACAA 5 15 1 TAACAAGCGC 0.919393 -260 AACGCGAGTTGAAAAACTCGCGTTATTTTAT 7 27 1 GAAAACTCGC 0.961408 -46 AATAAGTGCGGATAAAATAACGCGAGTTTTT 7 38 0 GAAAAATAAC 0.870181 -35 CCTCTGTGATAAAAGCGCTGACTATTCT 10 87 0 GAAAAAGCGC 0.995065 -18 ** ******** Masking position 6 Map Score: 4.56608 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 262 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 GGCTATTTCAACAAATGCTGGTTTTTTGA 2 18 1 ACAAATGCGG 0.949121 -19 ATAACCCGATCCATCTGGAGGAACT 4 37 1 CCATCTGGGG 0.926166 -15 TAATATTACACCAACTGCGAATTATCGCCAG 5 70 0 CCAACTGCAA 0.982862 -205 CAAAATTTTGCCAAATGCAAAGCCTAAATAA 5 129 1 CCAAATGCAA 0.96524 -146 AAATTTCGCTCCAAATGGCAAAATATACACA 5 232 1 CCAAATGGAA 0.954835 -43 AGCAATCAAAACAACTGGGGATTAATCCTT 6 10 0 ACAACTGGGA 0.977609 -61 GCTAAAACAAACAACTTCTGATATTTATACC 9 117 0 ACAACTTCGA 0.881491 -142 ******** ** Masking position 3 Map Score: 3.22597 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 573 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 GTTTTTTACTCAAACTTGAACGAGAGAAAA 1 2 1 TTTTCTTTAA 0.984169 -128 ACGTCTAATATTAGTTTCTTAAGGTTAAGTTAATATTCT 5 186 1 TTTTCTTTAG 0.977263 -89 CCCAGTTGTTTTGATTGCTTGCCGATAAAGCTGAAATAT 6 22 1 TTTTCTATAA 0.929075 -49 AATTTATTCCTTATTCTTTAATATTTCAGCT 6 50 0 TTTTCTTTAA 0.974935 -21 ATTTCACGACTTCCTGTCTTGTTATTTTAGTTTGTTCCT 9 45 1 TTTGCTTTTA 0.89923 -214 TTTTAGTTTGTTCCTGACTGCTATTTTAGGAACCCAATT 9 69 1 TTTGCTTTAG 0.966582 -190 TTTATTTCCTCTTTGTTAAACAAAAATGTG 10 2 1 TTTTCTTTAA 0.984585 -103 ** ** ** ** ** Masking position 9 Map Score: 3.89055 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 39 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 CTTTTCTCTCGTTCAAGTTTGAGTAAAAAA 1 12 0 GTTCAAGTTT 0.878159 -118 GCAGCTTCCAGTTCCAGATTAGAGAAATGA 1 61 0 GTTCCAGATT 0.917686 -69 TTCGCAGTTGGTGTAATATTAAAAATCCTA 5 80 1 GTGTAATATT 0.942567 -195 AATATAAAAATTTCAATATTTACGTCTAAT 5 165 1 TTTCAATATT 0.818502 -110 CAATATTTACGTCTAATATTAGTTTCTTAA 5 178 1 GTCTAATATT 0.859593 -97 ATTCCTTATTCTTTAATATTTCAGCTTTAT 6 46 0 CTTTAATATT 0.723196 -25 GGTACAATGCGTGCAATTTTTACTATTAGA 8 13 1 GTGCAATTTT 0.938913 -28 CAAAAATGTGGTGCCATATTAAAGATTAGT 10 31 1 GTGCCATATT 0.959637 -74 ********** Masking position 6 Map Score: 2.30342 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 254 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 TATATTTGCTATAAAGAGTGTTGTGTATAT 5 254 0 ATAAAGAGTG 0.948929 -21 TTGATTATCGAAAACGCGAGTTGAAAAACT 7 15 1 AAAACGCGAG 0.932687 -58 TGCGGATAAAATAACGCGAGTTTTTCAACT 7 33 0 ATAACGCGAG 0.978535 -40 AAGGTACAATGCGTGCAATTTTTAC 8 6 1 ACAATGCGTG 0.933545 -35 TTCTGTATGTATTAGGAGTGAGAG 9 5 0 ATTAGGAGTG 0.89328 -254 TACATACAGAATTAAGCGTGGATTTCACGA 9 24 1 ATTAAGCGTG 0.967183 -235 ********** Masking position 4 Map Score: 1.00837 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 272 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 CTACGATGTCGGCAAAATGCCTCAAAATTT 5 107 1 GGCAAAATGC 0.951302 -168 CTTTGCATTTGGCAAAATTTTGAGGCATTT 5 121 0 GGCAAAATTT 0.984719 -154 GCCTAAATAAGAAAAAATATAAAAATTTCA 5 150 1 GAAAAAATAT 0.684456 -125 CGCTCCAAATGGCAAAATATACACAACACT 5 238 1 GGCAAAATAT 0.971862 -37 TAAATTTTCCTGAAAAATTTATTTTTACGA 9 151 1 TGAAAAATTT 0.828384 -108 CGATATGGATCGCAAAATTTGAAGCAACCG 9 178 1 CGCAAAATTT 0.936612 -81 CTAAAACAAGGGAAAGATTCTAGAATAGTC 10 66 1 GGAAAGATTC 0.865959 -39 ********** Masking position 5 Map Score: 1.94776 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 449 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 ********** No masking Map Score: -1.82309e-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: -1.82309e-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: -1.82309e-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