AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_hinf_reg_100.orf -o00360_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -x5 -e 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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #2 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #3 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #4 HI0301 300 hemolysin, putative #5 HI0468 300 ATP phosphoribosyltransferase (hisG) #6 HI0469 92 histidinol dehydrogenase (hisD) #7 HI0470 68 histidinol-phosphate aminotransferase (hisC) #8 HI0916 107 outer membrane protein, putative #9 HI1024 49 hexulose-6-phosphate synthase, putative #10 HI1027 58 L-xylulose kinase (lyx) #11 HI1028 30 conserved hypothetical protein #12 HI1030 71 conserved hypothetical transmembrane protein #13 HI1031 175 conserved hypothetical protein #14 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #15 HI1064 56 conserved hypothetical protein #16 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #17 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 ACGAGATCAATTCACAATCAAAAATCCATTATTCA 4 51 1 TTAATAAAAT 0.894471 -250 ATACTTTTCGTCATATAAACAAAATAAGAATATTT 4 105 1 TCTTAAAAAT 0.508902 -196 AGGGGAAAATTCTAGACAACAAAATATTCTTATTT 4 126 0 TCAAAAAAAT 0.9026 -175 TAAAGTGCGGTTAAAAATACACAATTTTTACGGAG 4 161 0 TTAATACAAT 0.750049 -140 TGATGTCTTATTGACGGCGAAAAATTATCATATTT 4 263 0 TTAGCAAAAT 0.690191 -38 AAAAAGCAATTTTTTTGAAAAAAATTGTGTTTTTA 5 25 0 TTTTAAAAAT 0.741198 -276 AAAAATACACTTTAAAATTAAAAAAAGCAATTTTT 5 46 0 TTAATAAAAA 0.791398 -255 TATCTCAACTTTAAAATAGGAAAAACATT 5 282 1 TTAAAAAAAA 0.921455 -19 ATTTAAATAATCAATATCTCAAAATGCTGGGTTAT 6 35 1 TCAACAAAAT 0.875492 -58 TTATTTTCCTTTGTATCCGTAAAATGGATGATAAC 6 65 0 TTTTCAAAAT 0.689536 -28 AGCAGTCAAATTTTCATACAACAATACGAAATATG 7 43 1 TTTAAACAAT 0.771586 -26 CTTCCTCATATTATTTAAGGAAAAACG 9 33 1 TTTTAAAAAA 0.566626 -17 TAGGCTGGATTTTACATAATAAAAATCCAGCCCAT 10 15 1 TTAAAAAAAA 0.921183 -44 ATATGAAATATTATCACAAGAAAATAGGATCTAGA 13 17 1 TTTAAAAAAT 0.905139 -159 GAAAATAGGATCTAGATCACAAAATCAGTAAAATT 13 36 1 TCAACAAAAT 0.875492 -140 AAATAAATTATTTATAAATCAATATGTTAAAATAA 13 69 0 TTAAAAATAT 0.60581 -107 AAAATTACGTTTCATAATTTACAAAAATAAGAAAG 13 125 0 TTAATACAAA 0.573521 -51 CTCTCTTAATTTTATATAGTAAAATTACGTTTCAT 13 145 0 TTAAAAAAAT 0.962918 -31 CTATATAAAATTAAGAGAGGAAAAA 13 161 1 TTAAAAAAAA 0.921455 -15 TTATACGATATTTATAGCTAAAAATAAAACGCACT 14 20 0 TTAACAAAAT 0.952059 -66 GTTGATACCTTACAAAAAATAAACAA 14 70 0 TTAACACAAA 0.759124 -16 ATCTCTCTATTTGAATAACCAAAATTGTGGCGATT 16 17 1 TTATAAAAAT 0.889253 -68 AAAATCTTTCTTGATAAAATAAAATGACTGAAGTA 17 74 1 TTAAAAAAAT 0.963198 -65 ** * * * ***** Masking position 1 Map Score: 25.1576 Number of sites scoring better than the average of aligned sites = 738 Number in coding regions = 516 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 TTAAAATTAATTACATTTTATT 3 35 1 TTACTTTTAT 0.549689 -12 GAATAATGGATTTTTGATTGTGAATTGATCT 4 54 0 TTTTGATTGT 0.716412 -247 ACAACAAAATATTCTTATTTTGTTTATATGA 4 115 0 ATTCTATTTT 0.836469 -186 TCCGTAAAAATTGTGTATTTTTAACCGCACT 4 162 1 TTGTTATTTT 0.823053 -139 CAATGTGCGGTTATTTTTTATTGATTTTCCT 4 206 1 TTATTTTTAT 0.369007 -95 TTTTATTGATTTTCCTCTTTTCGCGTTTTGC 4 221 1 TTTCTCTTTT 0.774956 -80 CTTTTCGCGTTTTGCGATTTTTTCTAAAATA 4 237 1 TTTGGATTTT 0.646977 -64 GGCGAAAAATTATCATATTTTAGAAAAAATC 4 252 0 TATCTATTTT 0.836469 -49 TTCAAAAAAATTGCTTTTTTTAATTTTAAAG 5 41 1 TTGCTTTTTT 0.717388 -260 TGCAGATAAAATTCATATTGTATATGCTCGC 5 110 0 ATTCTATTGT 0.709607 -191 ACTCGGAAGATATTTTATTATCTTCCAAACA 5 186 0 TATTTATTAT 0.587295 -115 TTTCGAGGGGTTTTCTTTTATCTCAACTTTA 5 264 1 TTTTTTTTAT 0.723763 -37 AATGTTTTTCCTATTTTAAAGTTGAGA 5 284 0 TTTCTATTTT 0.972989 -17 ACATATTTCGTATTGTTGTATGAAAA 7 53 0 TTTCTATTGT 0.945081 -16 AAATGATGGGTTTAATATTTTCTCTGCCCAA 8 68 0 TTTATATTTT 0.686787 -40 TATGGGCTGGATTTTTATTATGTAAAATCCA 10 20 0 ATTTTATTAT 0.587295 -39 ATGTGATTCGTTTTATATTATGGCGTTTTAC 12 27 0 TTTTTATTAT 0.909268 -45 TGTGATAATATTTCATATTGTGAA 13 4 0 TTTCTATTGT 0.945081 -172 TAAAATAATTTTACTGATTTTGTGATCTAGA 13 46 0 TTACGATTTT 0.711288 -130 TATAAATAATTTATTTATTTTACATTTATTG 13 88 1 TTATTATTTT 0.793891 -88 TTGACTGAGCTTTCTTATTTTTGTAAATTAT 13 116 1 TTTCTATTTT 0.972989 -60 TAAAATTACGTTTCATAATTTACAAAAATAA 13 130 0 TTTCTAATTT 0.650889 -46 AAATAAAATCTATCGGATTATACGATATTTA 14 41 0 TATCGATTAT 0.476492 -45 TAGATTTTATTTGTTTATTTTTTGTAAGGTA 14 60 1 TTGTTATTTT 0.823053 -26 TTAACCACGCTTTGATATTTTTAAATATTCA 17 36 0 TTTGTATTTT 0.856751 -103 ACTTCAGTCATTTTATTTTATCAAGAAAGAT 17 77 0 TTTTTTTTAT 0.723763 -62 **** ****** Masking position 9 Map Score: 20.279 Number of sites scoring better than the average of aligned sites = 1019 Number in coding regions = 710 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 270 Fraction of orfs with sites within 600 bp upstream = 0.0433665 Motif number 3 AATGTAATTAATTTTAACCGCACTTTTGCGCGC 3 19 0 ATTTACCGCC 0.986465 -28 AAATTGTGTATTTTTAACCGCACTTTAGGTTTA 4 169 1 TTTTACCGCC 0.90254 -132 AAATCAATAAAAAATAACCGCACATTGGGTTTA 4 200 0 AAATACCGCC 0.993238 -101 TGCACTTACCATCATCACCACACCTGATTATCT 5 137 1 ATATACCACC 0.965839 -164 TGTAAAAGCAATAAATACCCCTCGGAAGGCAAT 5 231 1 ATAAACCCCC 0.962084 -70 GTTGAGATAAAAGAAAACCCCTCGAAAATTGCC 5 258 0 AAAAACCCCC 0.9679 -43 CGTAAAATGGATGATAACCCAGCATTTTGAGAT 6 50 0 ATATACCCAC 0.833871 -43 TTATAGCTAAAAATAAAACGCACTCAATATAGC 14 11 0 AATAAACGCC 0.73105 -75 CTTATTCTATAAAATAACCGCTCAAGA 15 40 1 AAATACCGCC 0.993238 -17 TGTAAAAAATGACCGCACTTTTTGATGA 17 6 1 AAATACCGCC 0.993238 -133 GATTTTATAAAAATTAACCACGCTTTGATATTT 17 47 0 AATTACCACC 0.951945 -92 ** ** ***** * Masking position 7 Map Score: 15.9853 Number of sites scoring better than the average of aligned sites = 908 Number in coding regions = 558 Number in noncoding regions = 350 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 4 ACCATTTAGATTAGGGAAAAATA 1 14 1 TTAGGGAAAA 0.939573 -13 TCTCGTAAAAAGAGGGCAAAGATCCTTATC 4 27 0 AGAGGGCAAA 0.949496 -274 ATTTTTACGGAGAGGGGAAAATTCTAGACA 4 143 0 AGAGGGGAAA 0.949496 -158 AAACGCGAAAAGAGGAAAATCAATAAAAAA 4 219 0 AGAGGAAAAT 0.828527 -82 CAACTTTAAAATAGGAAAAACATT 5 287 1 ATAGGAAAAA 0.93612 -14 TGAGTTCTGATGAAGAAAAAAGTTCAATTT 8 12 0 TGAAGAAAAA 0.869034 -96 CTCATATTATTTAAGGAAAAACG 9 37 1 TTAAGGAAAA 0.869034 -13 TAAAATTAAGAGAGGAAAAA 13 166 1 AGAGGAAAAA 0.971703 -10 TTTTTAAGCCAGAAGGAAAAAACA 15 5 0 AGAAGGAAAA 0.971703 -52 CAACACATACATAAGGAAAAGCT 17 126 1 ATAAGGAAAA 0.93612 -13 ********** Masking position 3 Map Score: 11.6287 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 186 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 GAAAGCGCGCAAAAGTGCGGTTAAAATTAA 3 15 1 AAAAGTGCGG 0.975973 -32 TTATATGACGAAAAGTATCTATGTTGTGGA 4 93 0 AAAAGTATCT 0.558879 -208 CCTCTCCGTAAAAATTGTGTATTTTTAACC 4 158 1 AAAATTGTGT 0.951969 -143 GGTTTAAACCTAAAGTGCGGTTAAAAATAC 4 176 0 TAAAGTGCGG 0.837693 -125 TTTTTTGAAAAAAATTGTGTTTTTAGTACA 5 20 0 AAAATTGTGT 0.951969 -281 TTTTTTCAAAAAAATTGCTTTTTTTAATTT 5 37 1 AAAATTGCTT 0.838353 -264 AAACCCCTCGAAAATTGCCTTCCGAGGGGT 5 247 0 AAAATTGCCT 0.953716 -54 TTTATATAGTAAAATTACGTTTCATAATTT 13 140 0 AAAATTACGT 0.877377 -36 TCTGGCTTAAAAAATTGGCTTATTCTATAA 15 22 1 AAAATTGGCT 0.798442 -35 TTGAATAACCAAAATTGTGGCGATTTTACC 16 27 1 AAAATTGTGG 0.948812 -58 ATATTCATCAAAAAGTGCGGTCATTTTTTA 17 13 0 AAAAGTGCGG 0.975973 -126 ********** Masking position 4 Map Score: 11.9246 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 669 Number in noncoding regions = 322 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 6 CGGTTAAAATTAATTACATTTTATT 3 32 1 TAATACATTT 0.934493 -15 TTTGATGTGATAAGGATCTTTGCCCTCTTTT 4 19 1 TAAGATCTTT 0.814014 -282 ATAAACAAAATAAGAATATTTTGTTGTCTAG 4 119 1 TAAGATATTT 0.954467 -182 CGGCGAAAAATTATCATATTTTAGAAAAAAT 4 253 0 TTATATATTT 0.806288 -48 AATTGTGTTTTTAGTACATTTTTACTA 5 7 0 TTAGACATTT 0.877919 -294 ATATAAGATCTAATAACATTTGAGCGAGCAT 5 87 1 TAATACATTT 0.934099 -214 ATCATTTAATTAAGGATATTTATCAA 8 92 1 TAAGATATTT 0.95446 -16 AATATAAAACGAATCACATTTGTGATAATCA 12 39 1 GAATACATTT 0.859846 -33 TATTTTCTTGTGATAATATTTCATATTGTGA 13 12 0 TGATATATTT 0.777691 -164 CGCACTTTTTGATGAATATTTAAAAATATCA 17 24 1 GATGATATTT 0.559634 -115 **** ****** Masking position 6 Map Score: 5.08983 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 105 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 AATAAAATGTAATTAATTTTAACCGCACTTTT 3 25 0 AATATTTTAA 0.844835 -22 TTACACTCGGAAGATATTTTATTATCTTCCAA 5 189 0 AAAATTTTAT 0.893889 -112 TCACAAATGTGATTCGTTTTATATTATGGCGT 12 32 0 GATGTTTTAT 0.928468 -40 AAAATCAGTAAAATTATTTTAACATATTGATT 13 56 1 AATATTTTAA 0.844835 -120 CGTATAATCCGATAGATTTTATTTGTTTATTT 14 48 1 GAAATTTTAT 0.95566 -38 TATTCAAATAGAGAGATTTTAAA 16 2 0 GAAATTTTAA 0.918739 -83 ATTTTATCAAGAAAGATTTTATAAAAATTAAC 17 62 0 GAAATTTTAT 0.955646 -77 TTTTATACTTCAGTCATTTTATTTTATCAAGA 17 82 0 CATATTTTAT 0.858926 -57 GTTGTGTGATGAATAGTTTTATACTTCAGTCA 17 98 0 GATGTTTTAT 0.928467 -41 ** * ******* Masking position 7 Map Score: 4.79374 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 58 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TACTTACCTACAGCAAAACTTTAGA 2 70 1 CAGCAAAACT 0.902553 -15 TGAATTGATCTCGTAAAAAGAGGGCAAAGA 4 35 0 TCGTAAAAAG 0.764069 -266 TTTCCCCTCTCCGTAAAAATTGTGTATTTT 4 153 1 CCGTAAAAAT 0.896563 -148 TTAGAAAAAATCGCAAAACGCGAAAAGAGG 4 234 0 TCGCAAAACG 0.740048 -67 TAGTAAAAATGTACTAAAAA 5 1 1 TAGTAAAAAT 0.772642 -300 TCCTTTGTATCCGTAAAATGGATGATAACC 6 64 0 CCGTAAAATG 0.950349 -29 GACACGTAAGCAGTCAAATTTTCATACAAC 7 35 1 CAGTCAAATT 0.775184 -34 ATGAGGAAGGCAGTATAATTCTGTCTTTAA 9 12 0 CAGTATAATT 0.699362 -38 CAGCAATATGTTTCCAGTAA 12 1 1 CAGCAATATG 0.601055 -71 AATATGTTTCCAGTAAAACGCCATAATATA 12 15 1 CAGTAAAACG 0.950474 -57 ATCACAAAATCAGTAAAATTATTTTAACAT 13 51 1 CAGTAAAATT 0.952574 -125 TAATTTTATATAGTAAAATTACGTTTCATA 13 144 0 TAGTAAAATT 0.866282 -32 ********** Masking position 8 Map Score: 8.11278 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 312 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 TTTTGAAGTTTGATGTGATAAGGATCTT 4 9 1 TTTGATGTGA 0.847969 -292 ATAAGAATATTTTGTTGTCTAGAATTTTCC 4 128 1 TTTGTTGTCT 0.852114 -173 TTGATTTGTGTTTGATGTCTTATTGACGGC 4 280 0 TTTGATGTCT 0.948008 -21 ATTGATTTGTGTTTGATGTC 4 291 0 ATTGATTTGT 0.739508 -10 GAACGTTGTTTTTGAGTTCTGATGAAGAAA 8 24 0 TTTGAGTTCT 0.88446 -84 TGATAATCAATTGGAGGTGTA 12 61 1 TTGGAGGTGT 0.872101 -11 ATCCGATAGATTTTATTTGTTTATTTTTTG 14 54 1 TTTTATTTGT 0.638396 -32 TTATCGTAAATTTGAGTTGTGGTAAAATCG 16 47 0 TTTGAGTTGT 0.936925 -38 TCCTTATGTATGTGTTGTGTGATGAATAGT 17 113 0 TGTGTTGTGT 0.723169 -26 ********** Masking position 8 Map Score: 1.43533 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 267 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 TTGTGAATAATGGATTTTTGATTGTGAATT 4 59 0 TGGATTTTTG 0.939137 -242 GTAAAAATTGTGTATTTTTAACCGCACTTT 4 165 1 TGTATTTTTA 0.965278 -136 ATTGATTTGTGTTTGATGTCTTATT 4 286 0 TTTGTGTTTG 0.666503 -15 TGAAAAAAATTGTGTTTTTAGTACATTTTT 5 15 0 TGTGTTTTTA 0.940271 -286 AATTTTAAAGTGTATTTTTAAGGCAATATA 5 62 1 TGTATTTTTA 0.965278 -239 CAGGCGTGATTGTATGTTTGGAAGATAATA 5 172 1 TGTATGTTTG 0.939137 -129 TTTTATGGGCTGGATTTTTATTATGTAAAA 10 24 0 TGGATTTTTA 0.940271 -35 TTGAGTGCGTTTTATTTTTAGCTATAAATA 14 17 1 TTTATTTTTA 0.864104 -69 ********** Masking position 5 Map Score: 6.56144 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 110 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TAGAGTATACTACCCTAGGTACAGGA 2 7 0 TACCCTAGGT 0.991988 -78 TAGGGTAGTATACTCTAGGTTAGTTCTTCA 2 20 1 TACTCTAGGT 0.978436 -65 TAGGTAAGTATATCCTAGGTTCAGTCCTAT 2 50 0 TATCCTAGGT 0.978448 -35 ********** Masking position 7 Map Score: 0.00224368 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 ********** No masking Map Score: -2.24999e-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: -2.24999e-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: -2.24999e-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