AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_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 rfbA 57 glucose-1-phosphate thymidylyltransferase #2 rfbB 300 dTDP-glucose 4,6 dehydratase #3 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #4 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #5 HI0873 58 DTDP-glucose 4,6-dehydratase (rffG) #6 HI1537 251 lic-1 operon protein (licA) Motif number 1 AAGCGGCTCTCAGTTTGATTAATAGAGGTA 2 242 0 CAGTTTGATT 0.883485 -59 TATTACTTTCTTTTTTGATTTTAAGATAAG 4 89 1 TTTTTTGATT 0.952881 -212 AGATAAGGGATATTTTGATTTTATCTCTCT 4 112 1 TATTTTGATT 0.864692 -189 TATTTAAATTTTGTTTGATTTTAACACGTT 6 46 0 TTGTTTGATT 0.990357 -206 GATTGATTGATTGATTGATTGCATAGCATT 6 92 0 TTGATTGATT 0.992159 -160 GATTGATTGATTGATTGATTGATTGATTGA 6 104 0 TTGATTGATT 0.992159 -148 GATTGATTGATTGATTGATTGATTGATTGA 6 120 0 TTGATTGATT 0.992159 -132 GATTGATTGATTGATTGATTGATTGATTGA 6 140 0 TTGATTGATT 0.992159 -112 ATCCTACAATTTGATTGATTGATTGATTGA 6 152 0 TTGATTGATT 0.992159 -100 ********** Masking position 5 Map Score: 22.2242 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 19 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 AGATAAGATAAGATAAGATA 4 1 0 AGATAAGATA 0.988376 -300 AGATAAGATAAGATAAGATAAGATAAGATA 4 16 0 AGATAAGATA 0.988376 -285 GAAAAAGATAAGATAAGATAAGATAAGATA 4 26 0 AGATAAGATA 0.988376 -275 TTTGATTTTAAGATAAGGGATATTTTGATT 4 102 1 AGATAAGGGA 0.976386 -199 CTAAAATAGCGGATAAGAGAGATAAAATCA 4 127 0 GGATAAGAGA 0.976386 -174 ********** Masking position 5 Map Score: 7.11531 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 CATTAATACCTCTATTAATCAAACTGAGAGC 2 236 1 TCATTAATCA 0.982742 -65 TGCTATGCAATCAATCAATCAATCAATCAAT 6 94 1 TCATCAATCA 0.99726 -158 AATCAATCAATCAATCAATCAATCAATCAAT 6 110 1 TCATCAATCA 0.99726 -142 AATCAATCAATCAATCAATCAATCAATCAAT 6 122 1 TCATCAATCA 0.99726 -130 AATCAATCAATCAATCAATCAATCAATCAAT 6 134 1 TCATCAATCA 0.99726 -118 AATCAATCAATCAATCAATCAAATTGTAGGA 6 150 1 TCATCAATCA 0.99726 -102 ** ******** Masking position 5 Map Score: 18.8627 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 6 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 4 CATCATTCCTTTTAATTCATCTTGCTCCACCATCAC 1 30 0 TTTATCTTGT 0.531441 -28 TGTTGCGAATCTTCCTGCCGTTGTTT 2 1 1 TGGATCTTCT 0.805092 -300 TATTCAAAGTTTTCCAGGATTTTCCTTGTTTCCAGA 2 79 1 TTGATTTTCT 0.939594 -222 TGCCAGCAAATTCCAGGAATTTTCCTAACATCGCCA 3 84 0 TTGATTTTCT 0.939594 -156 CTGGTGGGTTTGGAACGGACTTTCCCTTCTGAATAA 3 163 1 TGGACTTTCC 0.82456 -77 GTTATACTTCTGCTAATAATTTTCTCTGAGAGCATG 3 210 1 TGTATTTTCC 0.96697 -30 ATCTTATCTTATCTTATCTTTTTCATTGTTCTAGTG 4 32 1 ATTTTTTTCT 0.439282 -269 TCTGCTTCCTTGCTTATTACTTTCTTTTTTGATTTT 4 75 1 TGTACTTTCT 0.857241 -226 AAGATAAGGGATATTTTGATTTTATCTCTCTTATCC 4 111 1 ATTATTTTAC 0.606611 -190 CTATTTTAGTATATTATGATTTTTTCGGGTGGGTAT 4 148 1 ATTATTTTTC 0.68843 -153 ATAGCTAACATTAGAGTAATTTTCATACAAATACTC 4 185 0 TTTATTTTCT 0.957649 -116 TTGGTAGGGTTTATTATTATTTTGTCCAATATTCTG 4 225 1 TTTATTTTGC 0.846851 -76 ATATAGTTTAAGGTATTAATTTTCCCTCCAGAATAT 4 253 0 AGTATTTTCC 0.926622 -48 TTTTAACACGTTAAAGTTATTTTTGTAAGGCTCTGA 6 22 0 TTTATTTTTT 0.818242 -230 ATATTTAAATTTTGTTTGATTTTAACACGTTAAAGT 6 41 0 TTTATTTTAC 0.781411 -211 ATTGATTGATTGCATAGCATTTTTGTATTCATTTTT 6 77 0 TGGATTTTTT 0.778937 -175 AGCCTGAGGAAGTATTTCATTTTCTTCATCAGCATT 6 200 1 AGTATTTTCT 0.917344 -52 ** * ****** * Masking position 12 Map Score: 10.5366 Number of sites scoring better than the average of aligned sites = 1070 Number in coding regions = 914 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 5 CGAGTTAGCAGTAGGGTTTTATTCAAAGTTT 2 60 1 GTGGGTTTTA 0.958052 -241 GGTAAGACAATTAGCGTTTGAATTTTTCGGG 2 122 1 TTGCGTTTGA 0.733646 -179 GTTTGAATTTTTCGGGTTTAGCGCGAGTGGG 2 137 1 TTGGGTTTAG 0.938326 -164 ACGTAAACACGTGGCGTTTTTGGCATAAGAC 3 15 0 GTGCGTTTTT 0.949764 -225 ACGTGTTTACGTGGCGTTTTGCTTTTATATC 3 34 1 GTGCGTTTTG 0.967729 -206 GCACAGGACTGGTGGGTTTGGAACGGACTTT 3 155 1 GGGGGTTTGG 0.978586 -85 GATTTTTTCGGGTGGGTATAGAGTATTTGTA 4 165 1 GGGGGTATAG 0.841893 -136 TATATATTTGGTAGGGTTTATTATTATTTTG 4 218 1 GTGGGTTTAT 0.982297 -83 GTTGGGTTAATAAATTTAAGG 5 48 0 GTGGGTTAAT 0.88646 -11 CAATCAAATTGTAGGATTTGTTAAAACTTGC 6 165 1 GTGGATTTGT 0.854101 -87 ** ******** Masking position 7 Map Score: 7.07823 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 428 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 ATTGATTGATTGATTGATTGCATAGCATTT 6 91 0 TGATTGATTG 0.996377 -161 ATTGATTGATTGATTGATTGATTGATTGAT 6 107 0 TGATTGATTG 0.996377 -145 ATTGATTGATTGATTGATTGATTGATTGAT 6 127 0 TGATTGATTG 0.996377 -125 ATTGATTGATTGATTGATTGATTGATTGAT 6 139 0 TGATTGATTG 0.996377 -113 TCCTACAATTTGATTGATTGATTGATTGAT 6 151 0 TGATTGATTG 0.996377 -101 ********** Masking position 5 Map Score: 17.2887 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 AGCGTGCATTAATACCTCTATTAATCAAAC 2 230 1 AATACCTCTA 0.967564 -71 AGTAATATGGAATAAATTAA 2 291 1 AATAAATTAA 0.636092 -10 TATAACCACGAAGACCTTTATTCAGAAGGG 3 186 0 AAGACCTTTA 0.917532 -54 ATTTTCATACAAATACTCTATACCCACCCG 4 173 0 AAATACTCTA 0.728293 -128 TTTGTATGAAAATTACTCTAATGTTAGCTA 4 190 1 AATTACTCTA 0.879835 -111 AGGGAAAATTAATACCTTAAACTATATAAA 4 262 1 AATACCTTAA 0.919538 -39 ATATATAGAGAAAACCTTTATATAGTTTAA 4 278 0 AAAACCTTTA 0.929756 -23 GTTGGGTTAATAAATTTAAGGTAATGCA 5 41 0 AATAAATTTA 0.846892 -18 GCCTTACAAAAATAACTTTAACGTGTTAAA 6 27 1 AATAACTTTA 0.965624 -225 ********** Masking position 7 Map Score: 4.9544 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 199 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 CTTCAGAGCATGCTGTGAAATAAGCGGCTC 2 263 0 TGCTGTGAAA 0.929558 -38 ATTTGTCTTATGCCAAAAACGCCAC 3 6 1 TCTTATGCCA 0.855769 -234 GCGCTGGCGATGTTAGGAAAATTCCTGGAA 3 80 1 TGTTAGGAAA 0.793275 -160 TTTGCTGGCATGTTATGCAATTTGCATATC 3 110 1 TGTTATGCAA 0.978581 -130 ATTAACCATTTGATATGCAAATTGCATAAC 3 121 0 TGATATGCAA 0.947625 -119 AACCCACCAGTCCTGTGCAAAAATTAACCA 3 143 0 TCCTGTGCAA 0.953298 -97 AATACAAAAATGCTATGCAATCAATCAATC 6 84 1 TGCTATGCAA 0.986278 -168 ********** Masking position 10 Map Score: 4.67251 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 176 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 CTACCAGAGCACTGCATGCATGCCTATGAT 2 181 0 ACTGCATGCA 0.981923 -120 TAGAGGTATTAATGCACGCTACCGCCCCTG 2 220 0 AATGCACGCT 0.981144 -81 CGCTTATTTCACAGCATGCTCTGAAGTAAT 2 267 1 ACAGCATGCT 0.981923 -34 AATGCATGCTCTCAGAGAAA 3 230 0 AATGCATGCT 0.988855 -10 ********** Masking position 6 Map Score: 2.17977 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 CCTGCCGTTGTTTTATATAAACCATCAGAAT 2 24 1 TTTTATATAA 0.772443 -277 GGCGTTTTGCTTTTATATCTGTAATCTTAAT 3 46 1 TTTTATATTG 0.955822 -194 TGTTCTAGTGCTTTATATCTGCTTCCTTGCT 4 58 1 CTTTATATTG 0.971445 -243 CTAATGTTAGCTATATATTTGGTAGGGTTTA 4 207 1 CTATATATTG 0.948008 -94 AAGGTTTTCTCTATATATGTA 4 290 1 CTATATATTA 0.92061 -11 TTGTATTCATTTTTATATTTAAATTTTGTTT 6 60 0 TTTTATATTA 0.932247 -192 ******** ** Masking position 6 Map Score: 1.54341 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 20 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 TTTTATATAAACCATCAGAATAACAACGAG 2 34 1 ACCATCAGAA 0.917504 -267 CCGTTCCAAACCCACCAGTCCTGTGCAAAA 3 151 0 CCCACCAGTC 0.947105 -89 AACGGACTTTCCCTTCTGAATAAAGGTCTT 3 176 1 CCCTTCTGAA 0.94128 -64 ATACTCTATACCCACCCGAAAAAATCATAA 4 161 0 CCCACCCGAA 0.987131 -140 TATTAATTTTCCCTCCAGAATATTGGACAA 4 246 0 CCCTCCAGAA 0.98916 -55 ********** Masking position 6 Map Score: 1.12961 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 279 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ********** No masking Map Score: -2.10077e-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 13 ********** No masking Map Score: -2.10077e-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 14 ********** No masking Map Score: -2.10077e-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