AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -icpxR9_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 GTAAAAGTGCTATAAAAGTGCGGTTTGTTT 1 35 0 TATAAAAGTG 0.670807 -68 GTTTTCCCTCTAAAAAATTAAGGGTTGTAT 1 80 0 TAAAAAATTA 0.906301 -23 ATGTTAAAAATAAAAAAAATTTGGCTTATG 3 12 1 TAAAAAAAAT 0.699524 -105 TGGTAGAACCTAAATAATTTCTTTTTTCTT 3 55 1 TAAATAATTT 0.64859 -62 TTTTTCTTGCTGAAAAAGTGCGGTTATAAT 3 77 1 TGAAAAAGTG 0.926078 -40 CTTTGAAAAATTTGCCGCAAATT 3 104 0 TGAAAAATTT 0.95712 -13 TTTTTAATCGTAAAAAATAGGCAAATGATA 4 35 0 TAAAAAATAG 0.911653 -52 AAATTCAATTTGAAAAATTACGTACAGAGG 5 39 1 TGAAAAATTA 0.88809 -262 AGGTAGATGATGAAAAATTTTTAGGTGTTA 5 66 1 TGAAAAATTT 0.95712 -235 TATCATCATTTAAAAAATTTAATCCTACTT 5 144 0 TAAAAAATTT 0.964547 -157 AGTTTTACTAAAAAAATGATCTGCCCAT 5 283 0 TAAAAAAATG 0.926712 -18 GGCTGAAAAGTTGTAACCTAACT 6 4 1 TGAAAAGTTG 0.763104 -177 AAACGAATATTAAAAAATATATGCACTTTG 6 56 0 TAAAAAATAT 0.877891 -125 GAAGTTTTTTTTAAAAATTTCCGTTTCTTA 6 86 1 TTAAAAATTT 0.836209 -95 AATTAGCATCTTAAAAAGTGAAAACTCCAT 8 113 0 TTAAAAAGTG 0.741295 -160 AATCTAAACGTAAAAAATTAGCATCTTAAA 8 128 0 TAAAAAATTA 0.906301 -145 TTGTTATAAATATAAAATTTTCCCGATTAT 8 158 0 TATAAAATTT 0.784048 -115 GAATGTTAATTGAAAAAATGCACAATTTAA 8 196 1 TGAAAAAATG 0.912081 -77 TTTTATTGACTAGAAAATTGCGCGTATTAG 9 21 1 TAGAAAATTG 0.814125 -173 GACAAAAAAATAAAAAAAATGTTCAATAAG 9 135 0 TAAAAAAAAT 0.699524 -59 ********** Masking position 1 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 GGTATCATAAGCCAAATTTTTTTTATTTTTA 3 16 0 GCAAATTTTT 0.937722 -101 TATAATTTGCGGCAAATTTTTCAAAG 3 101 1 GCAAATTTTT 0.937716 -16 AGTATCATTTGCCTATTTTTTACGATTAAAA 4 33 1 GCTATTTTTT 0.877485 -54 GGTAGATGATGAAAAATTTTTAGGTGTTATT 5 67 1 GAAAATTTTT 0.807206 -234 GCAAGTAGGATTAAATTTTTTAAATGATGAT 5 142 1 TAAATTTTTT 0.65912 -159 CCAATTTTTGTGCCACTTTTTGGAGCGTTAT 5 180 0 TCCACTTTTT 0.923786 -121 GCGGTCCAACTACCAATTTTTGTGCCACTTT 5 192 0 TCCAATTTTT 0.909397 -109 CCTACCCCCTGCCCACTTTCTTTTTCCCAAG 5 222 0 GCCACTTTCT 0.874475 -79 ATCTGCCCATGGCCATTTTTTTTCTACTGAT 5 262 0 GCCATTTTTT 0.987949 -39 GCCATGGGCAGATCATTTTTTTAGTAAAACT 5 280 1 GTCATTTTTT 0.967865 -21 CGTAAAGTGCGGTCATTTTTTGGCAAAATTT 8 15 1 GTCATTTTTT 0.967865 -258 AGGATGGAGTTTTCACTTTTTAAGATGCTAA 8 110 1 TTCACTTTTT 0.816624 -163 TTTTTAAGATGCTAATTTTTTACGTTTAGAT 8 126 1 GTAATTTTTT 0.914282 -147 TTGTTAAATTGTGCATTTTTTCAATTAACAT 8 198 0 GGCATTTTTT 0.931357 -75 TCCTCTTATTGAACATTTTTTTTATTTTTTT 9 131 1 GACATTTTTT 0.958531 -63 * ********* Masking position 5 Map Score: 20.4888 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 342 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 GTTTGTTTTTATTTCATTTTACGAGCTTAA 1 13 0 ATTTCATTTT 0.938541 -90 AACCTAAATAATTTCTTTTTTCTTGCTGAA 3 61 1 ATTTCTTTTT 0.980485 -56 TTTCATTGCTATTTCCTTTTTAATCGTAAA 4 51 0 ATTTCCTTTT 0.987607 -36 TGCTATTTCCTTTTTATTTCATTG 4 73 0 ATTTCCTTTT 0.987607 -14 CCCCTGCCCACTTTCTTTTTCCCAAGCGGT 5 218 0 CTTTCTTTTT 0.976439 -83 TTTTTTAAAAATTTCCGTTTCTTATTTGAC 6 92 1 ATTTCCGTTT 0.949031 -89 CATTCCGTGCCTTTCTTTTTGCCTGTTCGT 7 13 0 CTTTCTTTTT 0.976439 -118 ACGGAATGTGCTTTCTTTATTATTTGATCT 7 35 1 CTTTCTTTAT 0.867252 -96 TACTGCTCCGATTTCCTTTTAAACAAGATA 9 93 1 ATTTCCTTTT 0.987607 -101 ********** Masking position 4 Map Score: 18.2853 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 61 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 AAGTGCGGTTTGTTTTTATTTCATTTTACG 1 20 0 TGTTTTTATT 0.916043 -83 TCTTTTTATTTTCACCACAC 2 1 1 TCTTTTTATT 0.954286 -53 TAAGCCAAATTTTTTTTATTTTTAACATT 3 10 0 TTTTTTTATT 0.957121 -107 TAAATAATTTCTTTTTTCTTGCTGAAAAAG 3 65 1 CTTTTTTCTT 0.867468 -52 ATTGCTATTTCCTTTTTAATCGTAAAAAAT 4 47 0 CCTTTTTAAT 0.845222 -40 TGCTATTTCCTTTTTATTTCATTGCTAT 4 69 0 CCTTTTTATT 0.97488 -18 GGGCAGATCATTTTTTTAGTAAAACT 5 285 1 TTTTTTTAGT 0.92581 -16 GAATTGCGCTCTATTTTATTCACTCTTAAT 6 142 1 CTATTTTATT 0.815368 -39 AATGTGCTTTCTTTATTATTTGATCTTAAT 7 39 1 CTTTATTATT 0.815368 -92 AGAGATAGAGTTTTTTTAGTAGAAACAGGG 7 85 1 TTTTTTTAGT 0.92581 -46 ATTGCTGTATCGTTTTTAGTTG 8 261 1 CGTTTTTAGT 0.918964 -12 TTTTTGACCTTTTTATTGACTAGAAAA 9 8 1 CCTTTTTATT 0.97488 -186 TATTGAACATTTTTTTTATTTTTTTGTCTT 9 137 1 TTTTTTTATT 0.957121 -57 ********** Masking position 6 Map Score: 19.732 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 207 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 AAAGTGCTATAAAAGTGCGGTTTGTTTTTA 1 32 0 AAAAGTGCGG 0.988319 -71 TTCTTGCTGAAAAAGTGCGGTTATAATTTG 3 80 1 AAAAGTGCGG 0.988319 -37 AGTGCGGTTATAATTTGCGGCAAATTTTTC 3 93 1 TAATTTGCGG 0.917839 -24 TTTTATGACTAGAATTGCGCTCTATTTTAT 6 131 1 AGAATTGCGC 0.942575 -50 GAAGCGTAAAGTGCGGTCATTTTTTG 8 7 1 TAAAGTGCGG 0.984844 -266 TTGAGTTTGTTAAATTGTGCATTTTTTCAA 8 205 0 TAAATTGTGC 0.841618 -68 TATTGACTAGAAAATTGCGCGTATTAGAAC 9 24 1 AAAATTGCGC 0.981599 -170 ********** Masking position 3 Map Score: 8.79211 Number of sites scoring better than the average of aligned sites = 1300 Number in coding regions = 847 Number in noncoding regions = 453 Number of orfs with sites within 600 bp upstream = 301 Fraction of orfs with sites within 600 bp upstream = 0.0483456 Motif number 6 TTTTATAGCACTTTTACCTCGATTGTGGAAT 1 48 1 CTTTTACCTG 0.908065 -55 TTTGTTTTCCCTCTAAAAAATTAA 1 89 0 GTTTTCCCTT 0.869336 -14 TGGAGATTCCTTTTACCAATTATTCTTATT 2 34 0 CTTTTACCAT 0.930377 -20 ATTTTTTTTATTTTTAACATT 3 1 0 TTTTTAACAT 0.812312 -116 TTTCAAGTATCATTTGCCTATTTTTTACGAT 4 28 1 CATTTGCCTT 0.534656 -59 ATTTGCCTATTTTTTACGATTAAAAAGGAAA 4 39 1 TTTTTACGAT 0.648542 -48 TTTTTTAACTATGAAAATGAAG 5 2 1 TTTTTAACTT 0.870066 -299 TGATCAGTATCTTTTAACACTAAATCAGCGG 5 97 1 CTTTTAACAT 0.809146 -204 ACTACCAATTTTTGTGCCACTTTTTGGAGCG 5 184 0 TTTGTGCCAT 0.593698 -117 GCCCACTTTCTTTTTCCCAAGCGGTCCAACT 5 212 0 TTTTTCCCAG 0.855638 -89 GAACGCGTATTTTATGACTAGAATTGCGCTC 6 122 1 TTTATGACTG 0.432027 -59 CGTGCCTTTCTTTTTGCCTGTTCGTGA 7 7 0 TTTTTGCCTT 0.939388 -124 AGGGATAAGGCTTATCCCTGTTTCTACTAAA 7 99 0 CTTATCCCTT 0.858945 -32 AGGGATAAGCCTTATCCCTCTAAATTAAAA 7 111 1 CTTATCCCTT 0.858945 -20 TGAGGATGGAGTTTTCACTTTTTAAGATGCT 8 108 1 GTTTTCACTT 0.678541 -165 AGATGCTAATTTTTTACGTTTAGATTATAAT 8 132 1 TTTTTACGTT 0.740598 -141 AAATTTTATATTTATAACAAGGGTTATAGAA 8 168 1 TTTATAACAG 0.401025 -105 TTTTTGACCTTTTTATTGACTA 9 2 1 TTTTGACCTT 0.703035 -192 ********* * Masking position 3 Map Score: 9.25486 Number of sites scoring better than the average of aligned sites = 1220 Number in coding regions = 1026 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 7 ATGAAAATGAAGCTGCCAAAATTCAATTTGAAAAA 5 21 1 ATCAAAATTA 0.954741 -280 AAAGTTAGAGATACCTCAAAAGTTAGGTTACAACT 6 19 0 ACCAAAAGTA 0.883336 -162 AAATATATGCACTTTGCTAAAGTTAGAGATACCTC 6 37 0 ATCTAAAGTA 0.872012 -144 CTTCAAACGAATATTAAAAAATATATGCACTTTGC 6 55 0 ATAAAAATAA 0.754957 -126 TTTAATTTACCTAAATACAATTAAGAGTG 6 162 0 ATCTAAATAA 0.912791 -19 GATAAGCCTTATCCCTCTAAATTAAAA 7 114 1 ACCTAAATTA 0.943187 -17 TGCGGTCATTTTTTGGCAAAATTTAAATCAAAAGC 8 22 1 TTCAAAATTA 0.728289 -251 ACAAACTCAAAGATTTCTAAATTTATCTTAGGTTT 8 225 1 ATCTAAATTA 0.946673 -48 ACAAGTAGCAAATTCTATAAATTTATGTTCTAATA 9 45 0 ATATAAATTA 0.814722 -149 GTGGTCTGTAAGACAAAAAAATAAAAAAAATGTTC 9 141 0 ACAAAAATAA 0.742353 -53 AAATACTCCAAAATAAATTTCAGATAA 9 177 0 ACCAAAATAA 0.920835 -17 * * ******* * Masking position 9 Map Score: 5.83047 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 177 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 ATTTTAATCTATCATTATTTCAAGT 4 6 1 AATCTATCAT 0.87217 -81 AACACCTAAAAATTTTTCATCATCTACCTC 5 65 0 AATTTTTCAT 0.821561 -236 AGCGTTATTCAAATTATCATCATTTAAAAA 5 158 0 AAATTATCAT 0.941217 -143 TAAACGTAAAAAATTAGCATCTTAAAAAGT 8 124 0 AAATTAGCAT 0.809592 -149 AAGATTTCTAAATTTATCTTAGGTTTGATT 8 234 1 AATTTATCTT 0.962456 -39 AAATTCTATAAATTTATGTTCTAATACGCG 9 41 0 AATTTATGTT 0.831557 -153 AGAGGAGAGCAAATTATCTTGTTTAAAAGG 9 107 0 AAATTATCTT 0.9409 -87 CGTTATCTGAAATTTATTTTGGAGTATTT 9 175 1 AATTTATTTT 0.768508 -19 ********** Masking position 2 Map Score: 3.43916 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 137 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 CTTATGATACCCGATTATTTGGTAGAACCTAAAT 3 36 1 CCGTTATTTA 0.975665 -81 CTGAAAAAGTGCGGTTATAATTTGCGGCAAATTT 3 86 1 GCGTTATATG 0.858798 -31 TCCATTGATTCCGCTGATTTAGTGTTAAAAGATA 5 104 0 CCGTGATTTG 0.92343 -197 CTGCCCATGGCCATTTTTTTTCTACTGATAAAGA 5 257 0 CCATTTTTTA 0.797181 -44 TTAAAAATTTCCGTTTCTTATTTGACGAACGCGT 6 96 1 CCGTTCTATG 0.949679 -85 CCAAATATTGCCGCTTTTGATTTAAATTTTGCCA 8 35 0 CCGTTTTATA 0.970187 -238 TAAAATTTTCCCGATTATAATCTAAACGTAAAAA 8 142 0 CCGTTATATA 0.969539 -131 ACTTGTAAGACCGTTTTTGTACTGCTCCGATTTC 9 74 1 CCGTTTTTTG 0.980994 -120 TTGTACTGCTCCGATTTCCTTTTAAACAAGATAA 9 90 1 CCGTTTCTTA 0.903545 -104 *** **** * ** Masking position 5 Map Score: 4.26779 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 63 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 ********** 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 11 ********** 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 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