AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i188_Menaquinone_Biosynthesis_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 menD 88 2-oxoglutarate decarboxylase; SHCHC synthase #2 menF 300 isochorismate hydroxymutase 2, menaquinone biosynthesis #3 HI0282 60 conserved hypothetical protein #4 HI0285 135 menaquinone-specific isochorismate synthase (menF) #5 HI0967 25 H. influenzae predicted coding region HI0967 Motif number 1 TACCGATTCATATCAATAATCTATTTTTGTA 1 27 1 TATCATAATC 0.987705 -62 GTTTGTCCGGTATCAATATTGCGGCTAAGTA 1 66 0 TATCATATTG 0.987409 -23 GCATTCGGGTTATCGATATTCCTTTCCCTCT 2 156 1 TATCATATTC 0.993379 -145 TTATTATTTCTATCAATAATCCCTTCA 3 44 1 TATCATAATC 0.987705 -17 TACAAAATCTTTTCAATATTGAAAATTCAGC 4 65 0 TTTCATATTG 0.950855 -71 AAAAAATTAGCCATATTCTACCGCAGAT 4 118 0 TAGCATATTC 0.982099 -18 **** ****** Masking position 6 Map Score: 10.0418 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 40 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 TCCTTATACTTAGCCGCAATATTGATACCG 1 60 1 TAGCCGCAAT 0.978216 -29 GAGTTTGTCCGGTATCAATATTGCG 1 74 0 TGTCCGGTAT 0.793176 -15 TTTTTTGTAGTACCCCGTATAATGTGAGGC 2 35 1 TACCCCGTAT 0.867404 -266 ATGCCGGGTGTCGCCGGAATCTCTTGCGAC 2 130 0 TCGCCGGAAT 0.953416 -171 GGAATATCGATAACCCGAATGCCGGGTGTC 2 148 0 TAACCCGAAT 0.919121 -153 TTTGATGCCTTGAGCTGGCTGGCCAGTCAG 2 197 1 TGAGCTGGCT 0.611581 -104 TCAGCAAACATACCCGCAATTCTACTGGCA 2 223 1 TACCCGCAAT 0.971573 -78 GCTGTCGTCCTGGGCGCGATTACCCGTTTT 2 275 1 TGGGCGCGAT 0.93889 -26 GTATTCTGTAGGCGGGCTTTAGTCCGCC 3 9 1 TAGGCGGGCT 0.958644 -52 CAGCGTAAATTAACCGCACTTTTCTCGAAA 4 39 0 TAACCGCACT 0.931532 -97 GCGGTTAATTTACGCTGAATTTTCAATATT 4 52 1 TACGCTGAAT 0.87067 -84 ********** Masking position 1 Map Score: 7.7934 Number of sites scoring better than the average of aligned sites = 1952 Number in coding regions = 1793 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 3 CCGGTATCAATATTGCGGCTAAGTATAAGG 1 61 0 TATTGCGGCT 0.940183 -28 TAACAGGGAGAGGTCCGCGTGCAATCACTT 2 68 1 AGGTCCGCGT 0.957495 -233 CGATAACCCGAATGCCGGGTGTCGCCGGAA 2 141 0 AATGCCGGGT 0.949902 -160 TTGCCAGTAGAATTGCGGGTATGTTTGCTG 2 224 0 AATTGCGGGT 0.980284 -77 TAAAACGGGTAATCGCGCCCAGGACGACAG 2 276 0 AATCGCGCCC 0.899812 -25 TGGCGGACTAAAGCCCGCCTACAGAATAC 3 10 0 AAGCCCGCCT 0.940454 -51 AGGCGGGCTTTAGTCCGCCATATTTTATTA 3 20 1 TAGTCCGCCA 0.847631 -41 TTTTCGAGAAAAGTGCGGTTAATTTACGCT 4 38 1 AAGTGCGGTT 0.917321 -98 CAATATTGAAAATTCAGCGTAAATTAACCG 4 53 0 AATTCAGCGT 0.882115 -83 ********** Masking position 7 Map Score: 4.66041 Number of sites scoring better than the average of aligned sites = 1375 Number in coding regions = 1231 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 4 AAATGCAGTACCCCGGTGTAGGGAG 2 4 0 CCCCGGTTAG 0.994791 -297 TTTTGTAGTACCCCGTATAATGTGAGGCTTTT 2 37 1 CCCCGTAAAG 0.995162 -264 GCGGACCTCTCCCTGTTAAAAGCCTCACATTA 2 54 0 CCCTGTTAAG 0.982659 -247 GATTTTCCAGCGCCGTAGTAAGTGATTGCACG 2 85 0 CGCCGTATAG 0.988236 -216 GGGCGCGATTACCCGTTTTACGTCG 2 286 1 ACCCGTTTAG 0.987841 -15 ******* ** * Masking position 10 Map Score: 3.3884 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 68 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 GAGCTACAAAAATAGATTATTGATATGAAT 1 32 0 AATAGATTAT 0.949175 -57 CAAATGGCGCAGTAGATTTTCCAGCGCCGT 2 101 0 AGTAGATTTT 0.921613 -200 TTTGAGAGGGAAAGGAATATCGATAACCCG 2 161 0 AAAGGAATAT 0.726914 -140 CGTTGTTGCCAGTAGAATTGCGGGTATGTT 2 229 0 AGTAGAATTG 0.775528 -72 TGATAGAAATAATAAAATATGGCGGACTAA 3 29 0 AATAAAATAT 0.844889 -32 TATTAGAAACAAAAGGATTTCACT 4 5 0 AAAAGGATTT 0.795057 -131 TTTTGTTTCTAATAAATTTTTCGAGAAAAG 4 21 1 AATAAATTTT 0.920333 -115 TTCAATATTGAAAAGATTTTGTAAAAAAAT 4 73 1 AAAAGATTTT 0.939215 -63 TGTTAATGACAAAAAATTTTTTTACAAAAT 4 88 0 AAAAAATTTT 0.896769 -48 AAAAAATTAGCCATATTCTA 4 126 0 AAAAAATTAG 0.774189 -10 ********** Masking position 8 Map Score: 6.476 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 337 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 ********** No masking Map Score: 1.16772e-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 7 ********** No masking Map Score: 1.16772e-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 8 ********** No masking Map Score: 1.16772e-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