AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -icpxR6_hinf_opreg_300.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 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #2 HI0837 53 response regulator (cpxR) #3 HI0839 116 conserved hypothetical protein #4 HI0845 86 conserved hypothetical protein #5 HI0997 300 H. influenzae predicted coding region HI0997 #6 HI0998 180 ribosomal protein L34 (rpL34) #7 HI1002 130 thiophene and furan oxidation protein (thdF) #8 HI1004 272 peptidyl-prolyl cis-trans isomerse, putative #9 HI1259 193 periplasmic serine protease Motif number 1 AAACAAACCGCACTTTTATAGCACTTTTAC 1 35 1 CACTTTTATA 0.646542 -68 ATACAACCCTTAATTTTTTAGAGGGAAAAC 1 80 1 TAATTTTTTA 0.896722 -23 CATAAGCCAAATTTTTTTTATTTTTAACAT 3 12 0 ATTTTTTTTA 0.676354 -105 AAGAAAAAAGAAATTATTTAGGTTCTACCA 3 55 0 AAATTATTTA 0.623606 -62 ATTATAACCGCACTTTTTCAGCAAGAAAAA 3 77 0 CACTTTTTCA 0.918338 -40 AATTTGCGGCAAATTTTTCAAAG 3 104 1 AAATTTTTCA 0.952464 -13 TATCATTTGCCTATTTTTTACGATTAAAAA 4 35 1 CTATTTTTTA 0.902562 -52 CCTCTGTACGTAATTTTTCAAATTGAATTT 5 39 0 TAATTTTTCA 0.876902 -262 TAACACCTAAAAATTTTTCATCATCTACCT 5 66 0 AAATTTTTCA 0.952464 -235 AAGTAGGATTAAATTTTTTAAATGATGATA 5 144 1 AAATTTTTTA 0.960664 -157 ATGGGCAGATCATTTTTTTAGTAAAACT 5 283 1 CATTTTTTTA 0.919033 -18 AGTTAGGTTACAACTTTTCAGCC 6 4 0 CAACTTTTCA 0.743036 -177 CAAAGTGCATATATTTTTTAATATTCGTTT 6 56 1 ATATTTTTTA 0.865837 -125 TAAGAAACGGAAATTTTTAAAAAAAACTTC 6 86 0 AAATTTTTAA 0.82088 -95 ATGGAGTTTTCACTTTTTAAGATGCTAATT 8 113 1 CACTTTTTAA 0.720058 -160 TTTAAGATGCTAATTTTTTACGTTTAGATT 8 128 1 TAATTTTTTA 0.896722 -145 ATAATCGGGAAAATTTTATATTTATAACAA 8 158 1 AAATTTTATA 0.765208 -115 TTAAATTGTGCATTTTTTCAATTAACATTC 8 196 0 CATTTTTTCA 0.90303 -77 CTAATACGCGCAATTTTCTAGTCAATAAAA 9 21 0 CAATTTTCTA 0.797231 -173 CTTATTGAACATTTTTTTTATTTTTTTGTC 9 135 1 ATTTTTTTTA 0.676354 -59 ********** Masking position 5 Map Score: 23.3348 Number of sites scoring better than the average of aligned sites = 834 Number in coding regions = 578 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 2 TTTTAAGCTCGTAAAATGAAATAAAAACAAA 1 11 1 GAAAATGAAA 0.970539 -92 TGTAGTGTGGTGAAAATAAAAAGA 2 4 0 TAAAATAAAA 0.803553 -50 AGAATAATTGGTAAAAGGAATCTCCA 2 38 1 GAAAAGGAAT 0.921307 -16 AATGTTAAAAATAAAAAAAATTTGGC 3 6 1 TAAAATAAAA 0.803553 -111 TTTTCAGCAAGAAAAAAGAAATTATTTAGGT 3 62 0 GAAAAAGAAA 0.975954 -55 TTTTTACGATTAAAAAGGAAATAGCAATGAA 4 49 1 TAAAAGGAAA 0.980872 -38 AGCAATGAAATAAAAAGGAAATAGCA 4 71 1 TAAAAGGAAA 0.980872 -16 TTTTTAACTATGAAAATGAAGCTGCCAAAAT 5 12 1 TAAAATGAAG 0.858921 -289 GGACCGCTTGGGAAAAAGAAAGTGGGCAGGG 5 216 1 GAAAAAGAAA 0.975954 -85 TTTTTTCTACTGATAAAGAATACCCTACCCC 5 245 0 TATAAAGAAT 0.645729 -56 TCACGAACAGGCAAAAAGAAAGGCACGGAAT 7 11 1 GAAAAAGAAA 0.975954 -120 TAAGATCAAATAATAAAGAAAGCACATTCCG 7 36 0 TATAAAGAAA 0.890532 -95 ATTATCTTGTTTAAAAGGAAATCGGAGCAGT 9 94 0 TAAAAGGAAA 0.980872 -100 * ********* Masking position 6 Map Score: 19.6514 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 237 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 ATGAAGCTGCCAAAATTCAATTTGAAAAATTACGTAC 5 27 1 CAAAAAAGAA 0.863084 -274 AATAACGCTCCAAAAAGTGGCACAAAAATTGGTAGTT 5 179 1 CAAAAGGAAA 0.9593 -122 AGAGATACCTCAAAAGTTAGGTTACAACTTTTCAGCC 6 11 0 CAAAAAGAAA 0.969787 -170 ACGCGTTCGTCAAATAAGAAACGGAAATTTTTAAAAA 6 93 0 CAAATAAGAA 0.724914 -88 AAATAGAGCGCAATTCTAGTCATAAAATACGCGTTCG 6 121 0 CAATTGTAAA 0.705733 -60 TACCTAAATACAATTAAGAGTGAATAAAATAGAGCGC 6 147 0 CAATTAGAAA 0.884437 -34 TCTATCTCTACAAAATGCAGAATATATTAAGATCAAA 7 57 0 CAAAAAGAAT 0.857618 -74 CATTTTTTGGCAAAATTTAAATCAAAAGCGGCAATAT 8 28 1 CAAAAAAAAA 0.931965 -245 TGCATTTTTTCAATTAACATTCTATAACCCTTGTTAT 8 181 0 CAATTATAAA 0.765593 -92 ATTTTCTAGTCAATAAAAAGGTCAAAAA 9 2 0 CAATAAGAAA 0.948207 -192 CGGAGCAGTACAAAAACGGTCTTACAAGTAGCAAATT 9 66 0 CAAAAGTAAA 0.909572 -128 AAAAAATGTTCAATAAGAGGAGAGCAAATTATCTTGT 9 115 0 CAATAGGGAA 0.860848 -79 GTCTGTAAGACAAAAAAATAAAAAAAATGTTCAATAA 9 136 0 CAAAATAAAA 0.658407 -58 AAATACTCCAAAATAAATTTCAGATAACGTGGTCT 9 169 0 CAAAAATAAT 0.719927 -25 ***** ** * ** Masking position 3 Map Score: 7.95299 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 555 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 4 TATGATACCCGATTATTTGGTAGAACCTAA 3 38 1 GATTATTTGG 0.868219 -79 AAAGTGCGGTTATAATTTGCGGCAAATTTT 3 91 1 TATAATTTGC 0.968432 -26 TTATTTCAAGTATCATTTGCCTATTTTTTA 4 25 1 TATCATTTGC 0.932802 -62 TTTAAATGATGATAATTTGAATAACGCTCC 5 160 1 GATAATTTGA 0.93572 -141 AATTTCCGTTTCTTATTTGACGAACGCGTA 6 101 1 TCTTATTTGA 0.752519 -80 GTGCTTTCTTTATTATTTGATCTTAATATA 7 42 1 TATTATTTGA 0.919732 -89 CATAAATTTATAGAATTTGCTACTTGTAAG 9 53 1 TAGAATTTGC 0.891002 -141 TTTTAAACAAGATAATTTGCTCTCCTCTTA 9 109 1 GATAATTTGC 0.96767 -85 ********** Masking position 5 Map Score: 5.26351 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 98 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 AAGAATAATTGGTAAAAGGAATCTCCA 2 37 1 GGTAAAAGGA 0.768462 -17 CGATTAAAAAGGAAATAGCAATGAAATAAA 4 55 1 GGAAATAGCA 0.977644 -32 GAAATAAAAAGGAAATAGCA 4 77 1 GGAAATAGCA 0.977644 -10 AATGGATATGGCAAGTAGGATTAAATTTTT 5 132 1 GCAAGTAGGA 0.959201 -169 CACAAAAATTGGTAGTTGGACCGCTTGGGA 5 199 1 GGTAGTTGGA 0.84831 -102 TCTAACTTTAGCAAAGTGCATATATTTTTT 6 45 1 GCAAAGTGCA 0.774417 -136 CACAAAGCCAGCTAATAGCAATTCCTATCA 8 80 0 GCTAATAGCA 0.948771 -193 AAACGGTCTTACAAGTAGCAAATTCTATAA 9 60 0 ACAAGTAGCA 0.740592 -134 TTGTTTAAAAGGAAATCGGAGCAGTACAAA 9 89 0 GGAAATCGGA 0.915708 -105 ********** Masking position 4 Map Score: 5.16086 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 103 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 GTGCTATAAAAGTGCGGTTTGTTTTTATTT 1 29 0 AGTGCGGTTT 0.978092 -74 TTCTTATTGTAGTGTGGTGAAAATAAAAAG 2 12 0 AGTGTGGTGA 0.95593 -42 TTGCTGAAAAAGTGCGGTTATAATTTGCGG 3 83 1 AGTGCGGTTA 0.993239 -34 ATACCTCAAAAGTTAGGTTACAACTTTTCA 6 14 0 AGTTAGGTTA 0.87633 -167 GAAGCGTAAAGTGCGGTCATTTTTTGGCA 8 10 1 AGTGCGGTCA 0.988521 -263 ********** Masking position 3 Map Score: 3.32931 Number of sites scoring better than the average of aligned sites = 1032 Number in coding regions = 640 Number in noncoding regions = 392 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 7 TTTGTTTTCCCTCTAAAAAATTAAGGGT 1 85 0 TTTCCTAAAA 0.80941 -18 ATAAAAAAAATTTGGCTTATGATACCCGATTATT 3 21 1 TTTTATGATA 0.958662 -96 ATAATTTCTTTTTTCTTGCTGAAAAAGTGCGGTT 3 68 1 TTTTCTGAAA 0.85521 -49 CAAATGATACTTGAAATAATGATAGATTAAAAT 4 10 0 TTGTATGATA 0.82853 -77 ATTTGCCTATTTTTTACGATTAAAAAGGAAATAG 4 39 1 TTTCATTAAA 0.792406 -48 TTTTTTAACTATGAAAATGAAGCTGC 5 3 1 TTTCATGAAA 0.936822 -298 GATTAAATTTTTTAAATGATGATAATTTGAATAA 5 150 1 TTTTATGATA 0.953169 -151 ATGGCCATTTTTTTTCTACTGATAAAGAATACCC 5 251 0 TTTTCTGATA 0.961569 -50 AAATATAAAATTTTCCCGATTATAATCTAAACGT 8 147 0 TTTCATTATA 0.851634 -126 ATTCTATAAATTTATGTTCTAATACGCGCAATTT 9 35 0 TTTTCTAATA 0.851634 -159 *** * ****** Masking position 10 Map Score: 4.64743 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 160 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 TGCACTTTGCTAAAGTTAGAGATACCTCAA 6 35 0 TAAAGTTAGA 0.931119 -146 AAATGCAGAATATATTAAGATCAAATAATA 7 52 0 TATATTAAGA 0.830239 -79 TTTTAATTTAGAGGGATAAGGC 7 119 0 TTAATTTAGA 0.901256 -12 GGGAAAATTTTATATTTATAACAAGGGTTA 8 164 1 TATATTTATA 0.854082 -109 AAACCTAAGATAAATTTAGAAATCTTTGAG 8 230 0 TAAATTTAGA 0.97363 -43 TATTAGAACATAAATTTATAGAATTTGCTA 9 45 1 TAAATTTATA 0.925065 -149 ********** Masking position 6 Map Score: 1.43347 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 68 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 TTCCACAATCGAGGTAAAAGTGCTATAAAA 1 48 0 GAGGTAAAAG 0.973153 -55 TAATTTTTTAGAGGGAAAACAAA 1 90 1 GAGGGAAAAC 0.95867 -13 ATTACGTACAGAGGTAGATGATGAAAAATT 5 55 1 GAGGTAGATG 0.902529 -246 TTAGTAGAAACAGGGATAAGCCTTATCCCT 7 100 1 CAGGGATAAG 0.95867 -31 TTTTAATTTAGAGGGATAAGGCTTATCCCT 7 111 0 GAGGGATAAG 0.987904 -20 ********** Masking position 6 Map Score: 1.10987 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 15 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ACTGATAAAGAATACCCTACCCCCTGCCCAC 5 237 0 AATACCTACC 0.96504 -64 TTCTACTAAAAAAACTCTATCTCTACAAAAT 7 78 0 AAAACCTATC 0.978301 -53 TCCTATCAACAAAACACCACCAAATATTGCC 8 57 0 AAAACCCACC 0.990818 -216 TTAAAAAGTGAAAACTCCATCCTCACAAAGC 8 102 0 AAAACCCATC 0.985868 -171 ***** ***** Masking position 4 Map Score: 0.276283 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 21 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 TGCGGTTTGTTTTTATTTCATTTTACGAGC 1 17 0 TTTTATTTCA 0.945418 -86 TTTGTTTTCCCTCTAAAAAA 1 93 0 TTTGTTTTCC 0.755848 -10 TCTTTTTATTTTCACCACACTACA 2 5 1 TTTATTTTCA 0.75634 -49 GCCAAATTTTTTTTATTTTTAACATT 3 7 0 TTTTATTTTT 0.762791 -110 CTAAATAATTTCTTTTTTCTTGCTGAAAAA 3 64 1 TCTTTTTTCT 0.745678 -53 GCTATTTCCTTTTTATTTCATTGCTATTTC 4 66 0 TTTTATTTCA 0.945418 -21 CCCATGGCCATTTTTTTTCTACTGATAAAG 5 258 0 TTTTTTTTCT 0.933596 -43 TCGTTTGAAGTTTTTTTTAAAAATTTCCGT 6 80 1 TTTTTTTTAA 0.79846 -101 TATTGCCGCTTTTGATTTAAATTTTGCCAA 8 34 0 TTTGATTTAA 0.659451 -239 TGAACATTTTTTTTATTTTTTTGTCTTACA 9 140 1 TTTTATTTTT 0.762791 -54 ********** Masking position 6 Map Score: 3.99626 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 261 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 12 ********** No masking Map Score: 1.67931e-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: 1.67931e-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: 1.67931e-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