AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i346_weak7_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 yfhE 95 orf, hypothetical protein #2 b2529 27 orf, hypothetical protein #3 yfhO 87 putative aminotransferase #4 b2531 177 orf, hypothetical protein #5 HI0372 39 ferredoxin (fdx-1) #6 HI0374 50 H. influenzae predicted coding region HI0374 #7 HI0376 56 conserved hypothetical protein #8 HI0377 59 iscU protein (iscU) #9 HI0378 60 nifS protein (nifS) #10 HI0379 52 conserved hypothetical protein #11 HI0380 300 conserved hypothetical protein Motif number 1 GGCGACCACGGTGGGGTTATCGGTATGCGC 1 12 0 GTGGGGTTAT 0.977098 -84 TACTCCGTAAACACGGTCGTACATCCAGCC 3 45 1 ACACGGTCGT 0.616229 -43 TGACTGATTTAGTCGGGTATTTAACCTTCA 4 45 0 AGTCGGGTAT 0.657322 -133 GTATTGCATAGCAGGGTCAAGTCTGACATT 4 102 0 GCAGGGTCAA 0.900555 -76 TATTGTAAAAGTGGGGGTATTGCATAGCAG 4 118 0 GTGGGGGTAT 0.979816 -60 AAAACCCCGGGCAGGGGCGAGTTTGAGGTG 4 149 1 GCAGGGGCGA 0.901972 -29 ATGTGGGGGCAAATGTAATTTG 6 3 1 GTGGGGGCAA 0.982318 -48 TTCACATCTCGTAGGGGCAAATTACATTTG 6 20 0 GTAGGGGCAA 0.953295 -31 ATGTGAAAAAGTGCGGTCAATTTTGACCGC 7 13 1 GTGCGGTCAA 0.964297 -44 ACCGCTAAAAATGCGGTCAAAATTGACCGC 7 25 0 ATGCGGTCAA 0.843971 -32 TTTTAGCGGTGTTGGGGGATAG 7 45 1 GTTGGGGGAT 0.873985 -12 TAATAAAAAAGTGCGGTTATATTTAGCATA 9 33 1 GTGCGGTTAT 0.959351 -28 ATTTAATACAGTGGGGTCGTTAGCTCAGTC 11 13 1 GTGGGGTCGT 0.987365 -288 ATCAGAGAGTGGTGGGTCGTGAAGGATTCG 11 81 0 GGTGGGTCGT 0.965365 -220 TAGTTGTCCAGTTGGGTTGTTAGCTCAGTT 11 112 1 GTTGGGTTGT 0.953473 -189 TAATAAAAATGGTGGGTTGTGAGAGACTAG 11 180 0 GGTGGGTTGT 0.931452 -121 CTTAAATTTTAGTCGGGTATCATT 11 287 1 AGTCGGGTAT 0.657322 -14 ********** Masking position 5 Map Score: 25.1231 Number of sites scoring better than the average of aligned sites = 1906 Number in coding regions = 1730 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 CGGCGGATCGCAGCCCTGAGAATGTT 1 80 1 CAGCCCTGAG 0.980936 -16 AATTCAGAATCAGGCCGGAGTGCTAAATAC 3 18 1 CAGGCCGGAG 0.991194 -70 GTCGTACATCCAGCCGGTAGCCTGATTCCT 3 60 1 CAGCCGGTAG 0.992099 -28 TCAAGTCTGACATTCCCGAGTAAATTGGTC 4 86 0 CATTCCCGAG 0.904475 -92 AAACTCGCCCCTGCCCGGGGTTTTTTATTG 4 143 0 CTGCCCGGGG 0.935663 -35 TATTTATTCACATCTCGTAGGGGCAAATTA 6 26 0 CATCTCGTAG 0.886745 -25 GTCGTTAGCTCAGTCGGTAGAGCAGCGGAC 11 28 1 CAGTCGGTAG 0.99013 -273 GTTGTTAGCTCAGTTGGTAGAGTAGCGGAC 11 127 1 CAGTTGGTAG 0.952905 -174 CTTAATCCGTCAGTCGAGAGTTCTAGTCTC 11 158 1 CAGTCGAGAG 0.963081 -143 ********** Masking position 1 Map Score: 10.6452 Number of sites scoring better than the average of aligned sites = 935 Number in coding regions = 868 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 CAGGCCGGAGTGCTAAATACTCCGTAAACA 3 28 1 TGCTAAATAC 0.694005 -60 ACAAACGCCACGATAAAAAAATGGCACTGA 4 18 1 CGATAAAAAA 0.926732 -160 CCCACTTTTACAATAAAAAACCCCGGGCAG 4 133 1 CAATAAAAAA 0.805653 -45 AATACTTTCCTCAAAATTATTTAATAT 5 23 0 TCCTCAAAAT 0.823729 -17 GCTAAAAATGCGGTCAAAATTGACCGCACT 7 22 0 CGGTCAAAAT 0.828462 -35 CCCCCAACACCGCTAAAAATGCGGTCAAAA 7 33 0 CGCTAAAAAT 0.984953 -24 GTATATTTTTTAATAAAAAAGTGCGGTTAT 9 23 1 TAATAAAAAA 0.68549 -38 TCCTAAATTATGCTAAATATAACCGCACTT 9 41 0 TGCTAAATAT 0.895168 -20 AAAGAATCCCTAAAAATTAATTGCGCA 10 36 0 CCCTAAAAAT 0.958606 -17 TAGGGATGAATAATAAAAATGGTGGGTTGT 11 190 0 TAATAAAAAT 0.827985 -111 CCACAATAACCGCTAAAAATAGTCAAGAAT 11 248 0 CGCTAAAAAT 0.984953 -53 ********** Masking position 6 Map Score: 7.59783 Number of sites scoring better than the average of aligned sites = 870 Number in coding regions = 694 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 4 TCGGTATCGGAATCAGGAGAATTTAT 2 7 1 TCGGAATCAG 0.942803 -21 TAAAAAGAATTCAGAATCAGGCCG 3 5 1 AAGAATTCAG 0.929823 -83 TCAATGCAAGGAATCAGGCTACCGGCT 3 71 0 AAGGAATCAG 0.954624 -17 TAAATACCCGACTAAATCAGTCAAGTAAAT 4 52 1 ACTAAATCAG 0.957747 -126 TACATATCTGACTAATTTAG 10 1 0 ACTAATTTAG 0.778108 -52 CCTTCGACCAACGGATTAAAAGTCCGCTGC 11 49 0 ACGGATTAAA 0.736977 -252 CAACTGGACAACTAAATCAGAGAGTGGTGG 11 96 0 ACTAAATCAG 0.957747 -205 CTCTCGACTGACGGATTAAGAGTCCGCTAC 11 148 0 ACGGATTAAG 0.961673 -153 ********** Masking position 5 Map Score: 5.33816 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 606 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 TCAGGGCTGCGATCCGCCGCGATAACGGCGAATCAGGTA 1 60 0 GTCCCCTACC 0.9944 -36 GTCTTACTTCACCTCAAACTCGCCCCTGCCCGGG 4 154 0 ATTCCCACCC 0.969729 -24 ACGGATTAAAAGTCCGCTGCTCTACCGACTGAGCTAACG 11 30 0 ATCCCCTACC 0.996225 -271 GTTGGTCGAAGGTTCGAATCCTTCACGACCCACCACTCT 11 67 1 GTTCACTCCC 0.96589 -234 ACGGATTAAGAGTCCGCTACTCTACCAACTGAGCTAACA 11 129 0 ATCCCCTACC 0.996225 -172 GTCAGTCGAGAGTTCTAGTCTCTCACAACCCACCATTTT 11 166 1 ATTCACTCCC 0.97679 -135 ATTTAAGGGTATTCTACCACAATAACCGCTAAAAATAGT 11 255 0 ATCTCCTACC 0.971616 -46 * *** * * ** * * Masking position 3 Map Score: 5.56994 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 245 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TACCTGATTCGCCGTTATCGCGGCGGATCG 1 60 1 GCCGTTATCG 0.919967 -36 CGTACATCCAGCCGGTAGCCTGATTCCTTG 3 62 1 GCCGGTAGCC 0.968146 -26 ATACAGTGGGGTCGTTAGCTCAGTCGGTAG 11 18 1 GTCGTTAGCT 0.978022 -283 CGTTAGCTCAGTCGGTAGAGCAGCGGACTT 11 30 1 GTCGGTAGAG 0.987178 -271 GTCCAGTTGGGTTGTTAGCTCAGTTGGTAG 11 117 1 GTTGTTAGCT 0.955646 -184 TGTTAGCTCAGTTGGTAGAGTAGCGGACTC 11 129 1 GTTGGTAGAG 0.973878 -172 AAAATGGTGGGTTGTGAGAGACTAGAACTC 11 175 0 GTTGTGAGAG 0.904759 -126 ********** Masking position 7 Map Score: 5.31888 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 720 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 GATAACGGCGAATCAGGTAAAACAAACCCC 1 49 0 AATCAGGTAA 0.911578 -47 TGACTGATTTAGTCGGGTATTTAACCTTCA 4 45 0 AGTCGGGTAT 0.988215 -133 CGACTAAATCAGTCAAGTAAATAGTTGACC 4 60 1 AGTCAAGTAA 0.954784 -118 AACTGCAGTCAGATATTAAATAATTT 5 7 1 AGTCAGATAT 0.98302 -33 TGAATGCCATTGTCAGATAATGGCAACTAA 8 14 0 TGTCAGATAA 0.866079 -46 CTAAATTAGTCAGATATGTAAGTATTG 10 8 1 AGTCAGATAT 0.98302 -45 CGCTAAAAATAGTCAAGAATTTAAGCTAAT 11 238 0 AGTCAAGAAT 0.858537 -63 CTTAAATTTTAGTCGGGTATCATT 11 287 1 AGTCGGGTAT 0.988215 -14 ********** Masking position 9 Map Score: 11.6326 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 193 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 AGGCGACCACGGTGGGGTTATCGGTATGCG 1 13 0 GGTGGGGTTA 0.962587 -83 GTCGCCTGCGCGTGGGGTTTGTTTTACCTG 1 36 1 CGTGGGGTTT 0.994118 -60 TCGCCGTTATCGCGGCGGATCGCAGCCCTG 1 68 1 CGCGGCGGAT 0.88845 -28 ATTTTTTTATCGTGGCGTTTGTACCTGTT 4 10 0 CGTGGCGTTT 0.986173 -168 TTATTGTAAAAGTGGGGGTATTGCATAGCA 4 119 0 AGTGGGGGTA 0.9537 -59 CTCGCCCCTGCCCGGGGTTTTTTATTGTAA 4 140 0 CCCGGGGTTT 0.956266 -38 CATTTAATACAGTGGGGTCGTTAGCTCAGT 11 12 1 AGTGGGGTCG 0.903914 -289 ********** Masking position 5 Map Score: 3.53399 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 386 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 ********** No masking Map Score: 1.57273e-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: 1.57273e-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 11 ********** No masking Map Score: 1.57273e-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