AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_hinf_reg_300.orf -o00550_hinf_300.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 HI0062 258 dnaK suppressor protein (dksA) #2 HI0063 247 poly(A) polymerase (pcnB) #3 HI0065 75 conserved hypothetical protein #4 HI0865 230 glutamine synthetase (glnA) #5 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #6 HI1129 201 conserved hypothetical protein #7 HI1130 30 conserved hypothetical protein #8 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #9 HI1137 21 cell division protein (ftsW) #10 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #11 HI1140 71 D-alanine--D-alanine ligase (ddlB) #12 HI1716 196 undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase (rfe), putative #13 HI1717 133 H. influenzae predicted coding region HI1717 #14 HI1718 56 H. influenzae predicted coding region HI1718 #15 HI1719 61 uridylyl transferase (glnD) Motif number 1 TGAAAAATACAAAAGTGCGGTTAAAATTAA 2 21 1 AAAAGTGCGG 0.992199 -227 TTAAATGCAAAAAAGTGCGGTTAATTTTAA 2 41 0 AAAAGTGCGG 0.992199 -207 TTTTGCATTTAAAAATGCAGGAAAATCCAC 2 59 1 AAAAATGCAG 0.951877 -189 TCTTGTAAAGAAAAAGGCAAGTGGATTTTC 2 79 0 AAAAAGGCAA 0.638139 -169 TCTTTACAAGAAAAGAGCCAAGTCATTTAT 2 98 1 AAAAGAGCCA 0.756213 -150 TATTTCCAACAACAAAACGGAGTAAATTAT 2 125 1 AACAAAACGG 0.584608 -123 TGAGGTTCATAAAAGTGCGGTGAAATTT 3 9 0 AAAAGTGCGG 0.992199 -67 TATGAACCTCAAAAGTGCGGTAGAATCAGC 3 28 1 AAAAGTGCGG 0.992199 -48 ATGAATGAAGAAAAATGTGGGCTGATTCTA 3 48 0 AAAAATGTGG 0.910773 -28 TTTTTTATGTAACAATGCAATAAAAATTGC 4 37 0 AACAATGCAA 0.505648 -194 TTGTTACATAAAAAATGGCGCAATGAATTG 4 52 1 AAAAATGGCG 0.929466 -179 TATATGCCCTAAACAAGCGGCTGTATTCTA 5 143 0 AAACAAGCGG 0.793065 -39 AAATTTTATGAAAAAAGCCGTTTGAATTGT 6 17 1 AAAAAAGCCG 0.954405 -185 TTATCAAAATAAAAAAGCCGTTTGAATAAA 6 46 0 AAAAAAGCCG 0.954405 -156 AGAAGTGGAGAAAAGTGGTGTTTTGTGGAG 6 136 1 AAAAGTGGTG 0.734809 -66 TACTAACGTAAAAAAGGTCGCTCTTTCAAA 8 39 0 AAAAAGGTCG 0.711214 -84 TTTTATATCCAAAAGTGCTAATATTAGAAA 10 51 1 AAAAGTGCTA 0.671661 -87 AAACTCAACTAAAAGTGCGGTTAAAATTCG 10 92 0 AAAAGTGCGG 0.992199 -46 AGATAGGCGTAAAAGTGCGGTCAATTTTGA 12 62 1 AAAAGTGCGG 0.992199 -135 TATTTTTATAAAAAATGCGGTCAAAATTGA 12 82 0 AAAAATGCGG 0.992824 -115 CATTTTTTATAAAAATACGGGCGTTGAAGT 12 95 1 AAAAATACGG 0.926733 -102 CGTTGAAGTGAAAAATAGGGCTTCGTTAAA 12 116 1 AAAAATAGGG 0.734168 -81 TTAAAAGGCGAACAAGGCGAACAAGGCGAA 13 12 1 AACAAGGCGA 0.798269 -122 GAACAAGGCGAACAAGGCGGACAAGGAGAA 13 39 1 AACAAGGCGG 0.960859 -95 AAAGAAAAACAAAAAGGGCGTAT 15 4 0 AAAAAGGGCG 0.87935 -58 ********** Masking position 2 Map Score: 46.3388 Number of sites scoring better than the average of aligned sites = 2110 Number in coding regions = 1505 Number in noncoding regions = 605 Number of orfs with sites within 600 bp upstream = 374 Fraction of orfs with sites within 600 bp upstream = 0.0600707 Motif number 2 AAAAATACAAAAGTGCGGTTAAAATTAACCGC 2 23 1 AAGTGCGGTA 0.998668 -225 AAATGCAAAAAAGTGCGGTTAATTTTAACCGC 2 37 0 AAGTGCGGTA 0.998668 -211 AGGTTCATAAAAGTGCGGTGAAATTT 3 5 0 AAGTGCGGTA 0.998668 -71 TGAACCTCAAAAGTGCGGTAGAATCAGCCCAC 3 30 1 AAGTGCGGTA 0.998668 -46 ACTCAACTAAAAGTGCGGTTAAAATTCGCAAC 10 88 0 AAGTGCGGTA 0.998668 -50 CCGAAGTGATGTGAATGGGGGGGGA 12 4 1 AAGTGATGTA 0.903399 -193 ATAGGCGTAAAAGTGCGGTCAATTTTGACCGC 12 64 1 AAGTGCGGTA 0.998668 -133 TTTTTATAAAAAATGCGGTCAAAATTGACCGC 12 78 0 AAATGCGGTA 0.9882 -119 ********* * Masking position 2 Map Score: 26.7925 Number of sites scoring better than the average of aligned sites = 886 Number in coding regions = 572 Number in noncoding regions = 314 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 3 CAATTTTTGCGGGCGGTATAAATATCAGAAG 1 146 0 GGGCGGTTAA 0.954514 -113 AAATACAAAAGTGCGGTTAAAATTAACCGCA 2 25 1 GTGCGGTAAA 0.997379 -223 ATGCAAAAAAGTGCGGTTAATTTTAACCGCA 2 36 0 GTGCGGTAAT 0.992873 -212 GTTCATAAAAGTGCGGTGAAATTT 3 4 0 GTGCGGTAAA 0.997379 -72 AACCTCAAAAGTGCGGTAGAATCAGCCCACA 3 32 1 GTGCGGTGAA 0.991532 -44 TCAACTAAAAGTGCGGTTAAAATTCGCAACG 10 87 0 GTGCGGTAAA 0.997379 -51 AGGCGTAAAAGTGCGGTCAATTTTGACCGCA 12 66 1 GTGCGGTAAT 0.992873 -131 TTTATAAAAAATGCGGTCAAAATTGACCGCA 12 77 0 ATGCGGTAAA 0.97701 -120 ******* *** Masking position 10 Map Score: 21.5373 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 360 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 4 ATATCAGAAGTTGTTTGTTTTAGCAAGTAAA 1 125 0 TTGTTTTTTT 0.81487 -134 TTAACCGCACTTTTTTGCATTTAAAAATGCA 2 47 1 TTTTTTCATT 0.612079 -201 CTCTTTTGATTTTTTTGTCTTCTTGCCAAAC 2 176 0 TTTTTTTCTT 0.917526 -72 TCAGCCCACATTTTTCTTCATTCATGACCCG 3 53 1 TTTTTCTCAT 0.726309 -23 ACATGTATAATTTTTCCTTTTCGACAAATGT 4 96 0 TTTTTCTTTT 0.956154 -135 TATACATGTATTTTTCTTTTTCTGCTATGAC 4 118 1 TTTTTCTTTT 0.956154 -113 ATGAAATTTATTTTTCTTATTCTAGTCATAG 4 142 0 TTTTTCTATT 0.858394 -89 TTCAAACGGCTTTTTTATTTTGATAAAAATC 6 50 1 TTTTTTTTTT 0.873714 -152 CTAGGTTCGCTCTTTCACTTTTGAAAGAGCG 8 20 1 TCTTTCCTTT 0.895256 -103 TTTCTTTCTTCTTAATTGCTATA 8 110 0 TCTTTCTCTT 0.943669 -13 TTATTTTTCCTTTTCTCCCAATGA 10 124 0 TTTTTCTTTT 0.956154 -14 TTCTATCCTGTTTTTCTTCTTACTGATGATA 11 50 0 TTTTTCTCTT 0.972273 -22 TTTACGCCTATCTTTTATTTTACCAGTGGTA 12 44 0 TCTTTTTTTT 0.767722 -153 CGAAGCCCTATTTTTCACTTCAACGCCCGTA 12 110 0 TTTTTCCTTC 0.667415 -87 CTTGTTCGCCTTGTTCGCCTTTTAAT 13 6 0 TTGTTCCCTT 0.948195 -128 CTTGTTCGCCTTGTTCGCCTTGTTCGCCTTG 13 24 0 TTGTTCCCTT 0.948195 -110 CAGATTTTCCTCGTTCTCCTTGTCCGCCTTG 13 51 0 TCGTTCCCTT 0.897372 -83 TACGCCCTTTTTGTTTTTCTTTATAATAAAA 15 12 1 TTGTTTTCTT 0.876205 -50 ****** **** Masking position 5 Map Score: 25.9913 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 535 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 5 GGCTGGAATTAATCTTTTATAAAA 1 2 0 ATCTTATAAA 0.891825 -257 AGCCTAGGCTAGTTTTATTTAAATATGCAAACG 1 41 1 ATTTTTTAAA 0.754532 -218 TAGCAAGTAAATTTTCCTGAAAAATTTATTTTT 1 103 0 ATTTTGAAAA 0.972156 -156 TTCATTCTATTGAAAAATACAAAAGT 2 4 1 ATCTTGAAAA 0.936632 -244 TGACTTGGCTCTTTTCTTGTAAAGAAAAAGGCA 2 90 0 CTTTTGTAAA 0.788927 -158 AAGAAAAATAAATTTCATGAAAAAATAGCATGG 4 155 1 ATTTTGAAAA 0.972194 -76 ACAAGTCACAAATCTTATAAAAATCTTTAAATT 5 84 1 ATCTTAAAAA 0.924034 -98 TCAATAAAATTTTATGAAAAAAGCCGTTTG 6 8 1 ATTTTGAAAA 0.972195 -194 CGGCTTTTTTATTTTGATAAAAATCAGTTGCTT 6 56 1 ATTTTAAAAA 0.966102 -146 GATTTTTAGAGATTTTCTAAAAATAAGTTCAAT 6 165 1 GTTTTAAAAA 0.893051 -37 AAATTTAAGATAAAAGTACTACAT 7 17 0 ATTTGATAAA 0.725693 -14 CAACGCCCGTATTTTTATAAAAAATGCGGTCAA 12 88 0 ATTTTAAAAA 0.966102 -109 GTGACCCTAAAATTTTTTGTAAAGGATAACATA 12 171 0 ATTTTGTAAA 0.959511 -26 ATATCTCTATTTTATTAAAAATATAAAACAA 14 9 1 ATTTTAAAAA 0.952643 -48 GATCGAAGTCGTTTTATTATAAAGAAAAACAAA 15 21 0 GTTTTATAAA 0.849533 -41 * *** ****** Masking position 11 Map Score: 19.7555 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 122 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 6 CCATATCGTAAAAATAAATTTTTCAGGAAAA 1 94 1 AAATAAATTT 0.874683 -165 TTTGTTTTAGCAAGTAAATTTTCCTGAAAAA 1 112 0 CAATAAATTT 0.957759 -147 AAGAAAAAGGCAAGTGGATTTTCCTGCATTT 2 71 0 CAATGGATTT 0.833653 -177 GTCTTCTTGCCAAACAAATTTTTGATATAAG 2 160 0 CAACAAATTT 0.827038 -88 TAGAATAAGAAAAATAAATTTCATGAAAAAA 4 149 1 AAATAAATTT 0.874683 -82 CGTCAAATCAAAATTGAATTTAAAGATTTTT 5 102 0 AAATGAATTT 0.661777 -80 TCAATAAAATTTTATGAAAAAA 6 2 1 CAAAAAATTT 0.761819 -200 CACATTAAAGCAACTGATTTTTATCAAAATA 6 65 0 CAATGATTTT 0.754739 -137 TACGCCTTAAAAATTGAACTTATTTTTAGAA 6 179 0 AAATGAACTT 0.781702 -23 TTACGTTAGTAAAGGAAATTTATATTTCCAT 8 58 1 AAAGAAATTT 0.804846 -65 GGCTTCGTTAAAAATATATTTCTAGGTAAAT 12 134 1 AAATATATTT 0.706534 -63 GGTAAATCAGAAACTGAATTTGTTGAG 13 117 1 AAATGAATTT 0.937204 -17 *** ******* Masking position 3 Map Score: 8.30575 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 146 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 TCCTGAAAAATTTATTTTTACGATATGGAT 1 92 0 TTTATTTTTA 0.46206 -167 CGCACTTTTGTATTTTTCAATAGAATGAA 2 10 0 TATTTTTCAA 0.679241 -238 AGCCAAGTCATTTATTTCCAACAACAAAAC 2 113 1 TTTATTTCCA 0.882849 -135 AATTGCACCCTACATTTCTACATTTGTCGA 4 77 1 TACATTTCTA 0.836989 -154 ATTATACATGTATTTTTCTTTTTCTGCTAT 4 116 1 TATTTTTCTT 0.797216 -115 TCATGAAATTTATTTTTCTTATTCTAGTCA 4 145 0 TATTTTTCTT 0.797216 -86 AAAGGAAATTTATATTTCCATCAATGATAT 8 68 1 TATATTTCCA 0.947443 -55 ATAAGTATTTTTTATATCCAAAAGTGCTAA 10 42 1 TTTATATCCA 0.42585 -96 TCGCAACGTTTTTATTTCTAATATTAGCAC 10 65 0 TTTATTTCTA 0.880886 -73 TTATTTTTCCTTTTCTCCCAA 10 127 0 TATTTTTCCT 0.800242 -11 TTACTGATGATACTTTTCTAATACTAAGAT 11 32 0 TACTTTTCTA 0.795882 -40 GCCTATCTTTTATTTTACCAGTGGTATCCT 12 40 0 TATTTTACCA 0.573967 -157 TCGTTAAAAATATATTTCTAGGTAAATTTG 12 138 1 TATATTTCTA 0.946484 -59 TTTGTTGTTTTATATTTTTAATAAAATAGA 14 16 0 TATATTTTTA 0.672626 -41 ********** Masking position 5 Map Score: 9.3676 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 290 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 AAATTTGAAGCAACCGTTTGCATATTTAAA 1 58 0 CAACCGTTTG 0.904012 -201 TAAATATCAGAAGTTGTTTGTTTTAGCAAG 1 129 0 AAGTTGTTTG 0.864173 -130 AAATAGAATACAGCCGCTTGTTTAGGGCAT 5 140 1 CAGCCGCTTG 0.971644 -42 TTTATGAAAAAAGCCGTTTGAATTGTTTAT 6 21 1 AAGCCGTTTG 0.99154 -181 CAAAATAAAAAAGCCGTTTGAATAAACAAT 6 42 0 AAGCCGTTTG 0.99154 -160 TGTTAGATCGAAGTCGTTTTATTATAAAGA 15 29 0 AAGTCGTTTT 0.863854 -33 ********** Masking position 8 Map Score: 4.42099 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 37 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 AAATTTTTCAGGAAAATTTACTTGCTAAAAC 1 109 1 GGAAATTTAC 0.875781 -150 ACAGGAAGTCGTGAAATCCACGCTTAATTCT 1 218 1 GTAAATCCAC 0.918981 -41 TAAAAATGCAGGAAAATCCACTTGCCTTTTT 2 68 1 GGAAATCCAC 0.967564 -180 CAAAAGTGCGGTAGAATCAGCCCACATTTTT 3 37 1 GTGAATCAGC 0.731598 -39 TATCACATTTGTAAAATCTAAAACATCCATT 5 54 0 GTAAATCTAA 0.862127 -128 TTCAAATTACGTCAAATCAAAATTGAATTTA 5 111 0 GTAAATCAAA 0.828243 -71 GATAACATAAGGCAAATTTACCTAGAAATAT 12 149 0 GGAAATTTAC 0.880758 -48 AGGAGAACGAGGAAAATCTGCTCATGAAAGT 13 62 1 GGAAATCTGC 0.968704 -72 AGCTAATCAAGGTAAATCAGAAACTGAATTT 13 107 1 GGAAATCAGA 0.886577 -27 ** ******** Masking position 6 Map Score: 3.75182 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 196 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 CAAACGGTTGCTTCAAATTTTGCGATCCATA 1 68 1 CTTAAATTTT 0.90812 -191 CATATCGTAAAAATAAATTTTTCAGGAAAAT 1 95 1 AAAAAATTTT 0.820495 -164 TCTTCTTGCCAAACAAATTTTTGATATAAGT 2 159 0 AAAAAATTTT 0.820495 -89 GCTATTTTTTCATGAAATTTATTTTTCTTAT 4 153 0 CATAAATTTA 0.90812 -78 TTATAAAAATCTTTAAATTCAATTTTGATTT 5 98 1 CTTAAATTCA 0.717057 -84 CGGCTTTTTTCATAAAATTTTATTGA 6 6 0 CATAAATTTT 0.949601 -196 TTCTTAATTGCTATAAATTTTAAAATTATAT 8 94 0 CTAAAATTTT 0.92411 -29 TTATCCTTTACAAAAAATTTTAGGGTCACAC 12 175 1 CAAAAATTTT 0.958693 -22 CTCAACAAATTCAGTTTCTGATT 13 121 0 CAAAAATTCA 0.856159 -13 *** ******* Masking position 6 Map Score: 3.66481 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 242 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 11 ATTTGCTTTTATACCTATTCAA 5 2 1 TTTCTTTTAT 0.869271 -180 TGGAGAAAAGTGGTGTTTTGTGGAGATTTTT 6 141 1 TGGGTTTTGT 0.956084 -61 AAAATAATGTAGTACTTTTATCTTAAATTT 7 11 1 AGTCTTTTAT 0.746685 -20 GGGTTGTGGCGTTTTATAAATAGCCTC 10 7 1 TGGGTTTTAT 0.944166 -131 GCACTTTTAGTTGAGTTTTGTCATTGGGAGA 10 104 1 TTGGTTTTGT 0.931749 -34 TTATTTTTCCTTTTCTCCCAATGACA 10 122 0 TTTCTTTTCT 0.708568 -16 CTAGGTAAATTTGCCTTATGTTATCCTTTAC 12 155 1 TTGCTTATGT 0.657645 -42 ACCTTTGTTTTGTTGTTTTATATTTTTAATA 14 23 0 TGTGTTTTAT 0.913822 -34 GTTAGATCGAAGTCGTTTTATTATAAAGAAA 15 27 0 AGTGTTTTAT 0.746685 -35 ATGAATTGCCTTTTGTTAGATCGAAG 15 46 0 TTGCTTTTGT 0.931749 -16 *** ******* Masking position 6 Map Score: 2.81921 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 141 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 GTGAAATCCACGCTTAATTCTGTATGTATT 1 228 1 CGCTTAATTC 0.936595 -31 CAAAAAAGTGCGGTTAATTTTAACCGCACT 2 34 0 CGGTTAATTT 0.902559 -214 GCTATTAGAACGCTCAACTCGTTTAGAATG 2 225 0 CGCTCAACTC 0.973574 -23 TTATAATGTGCGCTTATCTTAATAAGACTA 4 193 1 CGCTTATCTT 0.951745 -38 ATAATTTGTTCGCTCAACTTGCAAGTAATT 6 97 0 CGCTCAACTT 0.982063 -105 CGCACTTTTACGCCTATCTTTTATTTTACC 12 51 0 CGCCTATCTT 0.858534 -146 CGTAAAAGTGCGGTCAATTTTGACCGCATT 12 69 1 CGGTCAATTT 0.917937 -128 ********** Masking position 6 Map Score: 3.76641 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 71 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 ********** No masking Map Score: 5.92836e-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: 5.92836e-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 15 ********** No masking Map Score: 5.92836e-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