AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ityrR_hinf_opreg_100.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0287 116 tryptophan-specific transport protein (mtr) #2 HI0410 114 transcriptional regulatory protein (tyrR) #3 HI0471 111 imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (hisB) #4 HI0472 65 amidotransferase (hisH) #5 HI0473 35 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA) #6 HI0476 81 H. influenzae predicted coding region HI0476 #7 HI0477 29 tyrosine-specific transport protein (tyrP) #8 HI0528 36 tyrosine-specific transport protein (tyrP) #9 HI0530 231 O-sialoglycoprotein endopeptidase (gcp) #10 HI1288 300 ribosome binding factor A (rbfA) #11 HI1290 59 chorismate mutase / prephenate dehydrogenase (tyrA) #12 HI1547 217 phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine repressible) (aroG) Motif number 1 TGAATGCTTTGACAACATTACAAAGGGGACTAAAT 1 3 1 AATAAAAAAG 0.854655 -114 GTGCAATATATTTATATCGATAAAAAGGGGACATTTAGTCCCC 1 35 0 TTTAAAAACA 0.888872 -82 AAATTTGCACTATTATAGTAGTACACAAGGAAAGTGCAATATA 1 68 0 TATATAAAAA 0.911411 -49 AAAATGCCTCTAAAATAAATTTGCACTATTATAGT 1 92 0 AATAAAAGCA 0.464509 -25 AAAGTGTAAATATTATTTTACATAAGGTAAAAATGCGACCATT 2 31 0 TATAATAAAA 0.911506 -84 TCATTTGCTTTATACAAACAGTATAAAACTAAATAATCTCGAA 3 39 0 TATATAAAAA 0.911411 -73 CAATCGGTCGAATTTTGCAAAAATACGACAAAAATTAACCGCT 4 18 0 AATAAAAAAA 0.929402 -48 GGCAATTCAATATCATCGTAAAATACAGTGAAACT 6 57 1 TATAAAAAAA 0.909357 -25 ATTTTTTATTACATCATAAGGAAACAAAA 7 2 1 TTTAATAAAA 0.900081 -28 ACACAGGTGCTTTGGCAAAAATAAAATTTTAAATTGCAATTAA 9 37 0 TTTATAAAAA 0.900829 -195 ATCCTTTACTTTTTCCCTAAAAATAGATTAGAATTGCGTCCTT 9 99 0 TTTAAAAGAA 0.837383 -133 ATCGCGCAACATTTTAGGTAATAAATTAAGAAAATCA 9 205 1 ATTATAAAAA 0.812794 -27 TGCCCAAAGTTTTTCGTCTAAWTCATTTAAAAATGCTTGTTGT 10 46 1 TTTAWTAAAA 0.800371 -255 TCAGGTGTCATTTTATCGAAAAACAGTATTAAGTTGAAAGGGA 10 204 1 TTTAAAAAAG 0.918016 -97 ATCTTACATATATTGTAAAAAATTAATTACAAGGAGATTACTA 11 16 0 TATAATAAAG 0.821488 -44 AAACGAAATAATTAAGTAAATAAAAGATAAAAAAATACCGCAC 12 32 0 ATTAAAAAAA 0.922384 -186 TTCGATATGTTTTTTTAGAATAAAACCTACAAATTCCCTATTA 12 108 0 TTTAAAAAAA 0.959365 -110 TAAAAAAACATATCGAACTAGTTTACTAGTACAAAAATAAGTG 12 134 1 TATATTAACA 0.549467 -84 TTAGCTACATAATTTAAACACAACATTTGAAAGCAAGAGAGTA 12 181 1 AATAAAAAAG 0.854655 -37 *** * ** * *** Masking position 3 Map Score: 17.7021 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 570 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 2 ATAAAGTGCGGTCAAAAATGGTCGCATTTTT 2 15 1 GTCAAAAATG 0.806825 -100 TTTTACATAAGGTAAAAATGCGACCATTTTT 2 28 0 GGTAAAAATC 0.93985 -87 GCAAAAATACGACAAAAATTAACCGCTCTTT 4 14 0 GACAAAAATA 0.963444 -52 GGTCGAATTTTGCAAAAATACGACAAAAATT 4 25 0 TGCAAAAATC 0.924384 -41 CAGGTGCTTTGGCAAAAATAAAATTTTAAAT 9 46 0 GGCAAAAATA 0.972503 -186 AACATTTTAGGTAATAAATTAAGAAAATCA 9 212 1 GTAATAAATA 0.608796 -20 GTCTAAWTCATTTAAAAATGCTTGTTGTAAT 10 61 1 TTTAAAAATC 0.804814 -240 CAAGATTGTCGATAAAAATCACACATTACAA 10 85 0 GATAAAAATA 0.934107 -216 TCGTCTCGCTTGCATAAATTATGCCCTCTGT 10 132 1 TGCATAAATA 0.787299 -169 TCAAACTTCCGATAAAAATCACTTTACAGAG 10 157 0 GATAAAAATA 0.934107 -144 GAATTTAGCACGCAAAAATCCCTTTCAACTT 10 234 0 CGCAAAAATC 0.789982 -67 ATGAGGCGCTTTTATAAATAAGGAATAACT 10 281 1 TTTATAAATA 0.555255 -20 TACATATATTGTAAAAAATTAATTACAAGGA 11 24 0 GTAAAAAATA 0.862218 -36 ATATATGTAAGATAAAAATTACAG 11 46 1 GATAAAAATA 0.934107 -14 AAATAAAAGATAAAAAAATACCGCACTTTTG 12 27 0 TAAAAAAATC 0.71991 -191 AGTTTACTAGTACAAAAATAAGTGTAGATTA 12 153 1 TACAAAAATA 0.917294 -65 ********* * Masking position 6 Map Score: 14.9685 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 663 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 3 GGACATTTAGTCCCCTTTGTAATGTTGTCAAA 1 18 0 TCCCTTGTAA 0.992116 -99 GGACTAAATGTCCCCTTTTTATCGATATAAAT 1 37 1 TCCCTTTTAT 0.971841 -80 ATATTGCACTTTCCTTGTGTACTACTATAATA 1 69 1 TCCTTTGTAC 0.947328 -48 GTCGCATTTTTACCTTATGTAAAATAATATTT 2 35 1 TCCTTTGTAA 0.980069 -80 TGCGCGATTTTACCCTGTTTAAGCGGTTTTAA 9 181 0 TCCCTTTTAA 0.987552 -51 GCATAAATTATGCCCTCTGTAAAGTGATTTTT 10 143 1 TCCCTTGTAA 0.992116 -158 AGTTATTCCTTATTTATAAAAGCGCCT 10 284 0 TCCTTTTTAT 0.93099 -17 AACCTACAAATTCCCTATTAAACTATCTTTAC 12 96 0 TCCCTTTAAA 0.934282 -122 * **** ***** Masking position 11 Map Score: 12.2256 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 12 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TAAAATAATATTTACACTTTGTTGTAAAGA 2 54 1 TTTACACTTT 0.880237 -61 ATTATTTAGTTTTATACTGTTTGTATAAAG 3 45 1 TTTATACTGT 0.95088 -67 TGGTATGAGGTTTATCATTTGCTTTATACA 3 66 0 TTTATCATTT 0.836688 -46 TTTTTTATCCTTTTACAATCGGT 4 53 0 TTTATCCTTT 0.978668 -13 TGTGTTTGATCCTGTATGACTATAT 5 21 0 TTGATCCTGT 0.940078 -15 GAATTGGCATTCTATCCTTTACTTTTTCCC 9 125 0 TCTATCCTTT 0.914671 -107 GTTGCGCGATTTTACCCTGTTTAAGCGGTT 9 185 0 TTTACCCTGT 0.966524 -47 CCCTTTCAACTTAATACTGTTTTTCGATAA 10 216 0 TTAATACTGT 0.776244 -85 GCGGTATTTTTTTATCTTTTATTTACTTAA 12 34 1 TTTATCTTTT 0.836688 -184 ********** Masking position 4 Map Score: 7.57302 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 97 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 GTACACAAGGAAAGTGCAATATATTTATAT 1 61 0 AAAGTGCAAT 0.964385 -56 CGATATAAAGTGCGGTCAAAAATGGT 2 7 1 AAAGTGCGGT 0.992114 -108 TATTTAAGTCACAGAGCGATTCGAGATTAT 3 20 1 ACAGAGCGAT 0.940105 -92 TTGAAAGAGCGGTTAATTTTTGT 4 4 1 AAAGAGCGGT 0.985397 -62 ATAAAATTTTAAATTGCAATTAAATTAAAC 9 30 0 AAATTGCAAT 0.807294 -202 GTACAGCACAAAAGTGCGGTATTTTTTTAT 12 19 1 AAAGTGCGGT 0.992114 -199 ********** Masking position 3 Map Score: 7.17456 Number of sites scoring better than the average of aligned sites = 1245 Number in coding regions = 792 Number in noncoding regions = 453 Number of orfs with sites within 600 bp upstream = 309 Fraction of orfs with sites within 600 bp upstream = 0.0496306 Motif number 6 TGTTGTAAAGAAATTATCATAGCCATATCT 2 73 1 AAATTATCAT 0.937269 -42 AATACGACAAAAATTAACCGCTCTTTCAA 4 10 0 AAATTAACCG 0.81171 -56 GAAAATTGTCAGGCAATATTAA 6 3 1 AAATTGTCAG 0.973867 -79 AAAATTGTCCTTATAATGTTG 8 26 0 AAATTGTCCT 0.923904 -11 TCCTTTATTAAATTTGTCATTTACACACAG 9 74 0 AATTTGTCAT 0.886996 -158 TTGTTTGCGGAGTTTATCAGCAGATGCCCA 10 22 1 AGTTTATCAG 0.805096 -279 ATATTCAAACAAATTATCAGGTGTCATTTT 10 188 1 AAATTATCAG 0.968612 -113 ********** Masking position 1 Map Score: 3.03656 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 93 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AACTAAATAATCTCGAATCGCTCTGTGACT 3 26 0 TCTCGAATCG 0.979337 -86 ATCTTGGTCGTCTCGTCTCGTCTCGTCTCG 10 110 1 TCTCGTCTCG 0.995632 -191 TCTCGTCTCGTCTCGTCTCGCTTGCATAAA 10 120 1 TCTCGTCTCG 0.995632 -181 ********** Masking position 3 Map Score: 1.9574 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 0 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 TTGAAAGAGCGGTTAATTTTT 4 2 1 TGAAAGAGCG 0.967447 -64 GCATAATTTATGCAAGCGAGACGAGACGAG 10 126 0 TGCAAGCGAG 0.991602 -175 TTATTCAGCTTGCAAGAGAGTTGTAAAGAT 12 74 1 TGCAAGAGAG 0.995056 -144 AACATTTGAAAGCAAGAGAGTAATGT 12 202 1 AGCAAGAGAG 0.987603 -16 ********** Masking position 5 Map Score: 2.73645 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 CCCTTTGTAATGTTGTCAAAGCATTCA 1 8 0 TGTTGTCAAA 0.9223 -109 CATTTTTACCTTATGTAAAATAATATTTAC 2 39 1 TTATGTAAAA 0.721766 -76 ATTTACACTTTGTTGTAAAGAAATTATCAT 2 63 1 TGTTGTAAAG 0.978971 -52 TGTTTCCTTATGATGTAATAAAAAAT 7 7 0 TGATGTAATA 0.879535 -23 TAAAAATGCTTGTTGTAATGTGTGATTTTT 10 73 1 TGTTGTAATG 0.952967 -228 ATCTTACATATATTGTAAAAAATTAATTAC 11 29 0 TATTGTAAAA 0.854033 -31 CTTGCAAGAGAGTTGTAAAGATAGTTTAAT 12 82 1 AGTTGTAAAG 0.906308 -136 ********** Masking position 8 Map Score: 2.28688 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 126 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 ATTTAGTCCCCTTTGTAATGTTGTCAAAGC 1 16 0 CTTTGTAATG 0.837239 -101 CTTAATATTGCCTGACAATTTTC 6 4 0 CCTGACAATT 0.904641 -78 TTTTGTTTCCTTATGATGTAATAAAAAA 7 12 0 CCTTATGATG 0.941458 -18 AAAATTGTCCTTATAATGTTGTGTTTAA 8 19 0 CCTTATAATG 0.906437 -18 TAAAATGACACCTGATAATTTGTTTGAATA 10 189 0 CCTGATAATT 0.962784 -112 CTAGTAATCTCCTTGTAATTAATTTTTTAC 11 15 1 CCTTGTAATT 0.961981 -45 ********** Masking position 3 Map Score: 1.62814 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 63 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 ********** No masking Map Score: 2.51775e-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 12 ********** No masking Map Score: 2.51775e-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: 2.51775e-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