AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_hinf_reg_100.orf -o00520_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 HI0351 172 UDP-glucose 4-epimerase (galE) #2 HI0759 176 A/G-specific adenine glycosylase (mutY) #3 HI0812 21 glucosephosphate uridylyltransferase (galU) #4 HI0813 77 carbon storage regulator (csrA) #5 HI0814 187 alanyl-tRNA synthetase (alaS) #6 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #7 HI0825 145 H. influenzae predicted coding region HI0825 #8 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #9 HI0873 58 DTDP-glucose 4,6-dehydratase (rffG) #10 HI1354 300 glutaminyl-tRNA synthetase (glnS) #11 HI1355 65 conserved hypothetical protein #12 HI1356 61 4-alpha-glucanotransferase (malQ) #13 HI1358 95 glycogen operon protein (glgX) Motif number 1 GACTAAAAAATTATATCACTATTTTGTGTGGTAAG 1 124 0 TTAACCTTTT 0.882098 -49 ATAGAGCTTGTTTATCTGCATTTTTTCAGTATAAT 2 108 0 TTTTTCATTT 0.878297 -69 CATCAGCATTTTTAACCGCACTTTTCTTTTT 2 156 1 TTTACCATTT 0.933346 -21 TTTTATCTCCTTAGTTTGCATTTATTAGATATCCT 4 52 0 TTATTCATTT 0.676678 -26 TAACTTAAATTTTAACCGCACTTCTCAAATAGCGT 5 44 1 TTTACCATTT 0.933346 -144 AGTCGCCCTATTTTTGCATATTTTTGAAATTTATA 5 123 0 TTTTCTATTT 0.912991 -65 GCGACTTAGTTTTTATTTTTATTATGGGTAACAAG 5 152 1 TTTATTTTTT 0.808325 -36 AACTTTTTCCTTGTTATAATCTATAAA 6 3 1 CTTTCTTTTT 0.872515 -205 TTTTTATGATTTAGTTCATACTTATGAAAGTAACC 6 80 0 TTATCTATTT 0.752661 -128 AAAATTTTGCTTATTTTCTTATTTTGTGACAAAGA 6 112 1 TTATTTTTTT 0.652756 -96 ATTACATTAATTTATACTAAATTATTGTAAATAAA 6 153 0 TTTTCAATTT 0.91299 -55 TTTGACTCCTGTTTTTTATCAATGT 6 193 0 TTTATCTTTT 0.896375 -15 TTTGCCCACTTTTCATTCATTTTATTAAGATTGCG 7 17 0 TTTATATTTT 0.808325 -129 AGTGGGCAAATTTGTCCACTTTTGTTTTATCTATT 7 42 1 TTTTCCTTTT 0.975402 -104 TATCTTATCTTATCTTATCTTATCTTATCTTAT 8 9 1 CTTTTATTTT 0.696494 -292 CTTATCTTATCTTATCTTATCTTATCTTTTTCATT 8 24 1 CTTTTATTTT 0.696494 -277 CTTATCTTATCTTTTTCATTGTTCTAGTGCTTTAT 8 39 1 CTTTCTTTTT 0.872515 -262 GCTTCCTTGCTTATTACTTTCTTTTTTGATTTTAA 8 78 1 TTATCTTTTT 0.848631 -223 GATATTTTGATTTTATCTCTCTTATCCGCTATTTT 8 120 1 TTTACCTTTT 0.962684 -181 TTATTATTATTTTGTCCAATATTCTGGAGGGAAAA 8 235 1 TTTTCATTTT 0.950816 -66 TTATGGCAAGTTTTTACAATCTTTTATTTAAATCT 10 184 1 TTTTCATTTT 0.950816 -117 CAAACGTGATTTTGACCGCACTTTTTATTTGTATC 11 37 1 TTTACCATTT 0.933346 -29 ATTTTTATCGATTTTGTAGGCAAATTA 13 79 0 TTTACATTTT 0.926347 -17 *** * * ** ** * Masking position 12 Map Score: 27.9438 Number of sites scoring better than the average of aligned sites = 1016 Number in coding regions = 687 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 2 TCACTATTTTGTGTGGTAAGAATGGTGATTTT 1 112 0 GTGTGGTAAA 0.986953 -61 CACTCACGCGGTGTGGGGAGAAAGTTCCTATA 2 40 0 GTGTGGGAAA 0.952589 -137 AAAAAGAAAAGTGCGGTTAAAAATGCTGATGA 2 155 0 GTGCGGTAAA 0.996986 -22 TATTTGAGAAGTGCGGTTAAAATTTAAGTTAT 5 43 0 GTGCGGTAAA 0.996986 -145 GCGTCGTGAAGTGCGGTTTTATTTTGGAGTTT 5 75 1 GTGCGGTTAT 0.955943 -113 AATGCACAAAGTGCGGTAAGTTTTTTGAATGT 10 119 0 GTGCGGTATT 0.955943 -182 AATCAACCAAGTGCGGTCAAAACAAACGTGAT 11 15 1 GTGCGGTAAA 0.996985 -51 CAAATAAAAAGTGCGGTCAAAATCACGTTTGT 11 36 0 GTGCGGTAAA 0.996985 -30 ******* * ** Masking position 2 Map Score: 18.4016 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 303 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 GATTTTCAATAAAATAAAAAACCTGTTGCT 1 88 0 AAAATAAAAA 0.958723 -85 TATTTTATTGAAAATCACCATTCTTACCAC 1 102 1 AAAATCACCA 0.685164 -71 ATTTTCGTGTAAAATCATCAGCATTTTTAA 2 141 1 AAAATCATCA 0.856153 -36 CCAAAACTCCAAAATAAAACCGCACTTCAC 5 80 0 AAAATAAAAC 0.772112 -108 ACCCATAATAAAAATAAAAACTAAGTCGCC 5 151 0 AAAATAAAAA 0.958723 -37 AAGTATGAACTAAATCATAAAAAATTTTGC 6 92 1 TAAATCATAA 0.68574 -116 TCTTTGTCACAAAATAAGAAAATAAGCAAA 6 117 0 AAAATAAGAA 0.860512 -91 ATCAAAAAAGAAAGTAATAAGCAAGGAAGC 8 78 0 AAAGTAATAA 0.711077 -223 CCCTTATCTTAAAATCAAAAAAGAAAGTAA 8 91 0 AAAATCAAAA 0.965786 -210 TAAGAGAGATAAAATCAAAATATCCCTTAT 8 114 0 AAAATCAAAA 0.965786 -187 CCCACCCGAAAAAATCATAATATACTAAAA 8 151 0 AAAATCATAA 0.953499 -150 AATATTGGACAAAATAATAATAAACCCTAC 8 228 0 AAAATAATAA 0.944046 -73 TTCTCTCGTTAAAATAAAAAAATATTCGGC 10 280 0 AAAATAAAAA 0.958723 -21 AGTTGATACAAATAAAAAGTGCGGTCAA 11 48 0 CAAATAAAAA 0.785562 -18 ********** Masking position 7 Map Score: 17.5465 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 231 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 AAAGAAAAGTGCGGTTAAAAATGCTGATGA 2 155 0 GCGGTTAAAA 0.912411 -22 TTTGAGAAGTGCGGTTAAAATTTAAGTTAT 5 43 0 GCGGTTAAAA 0.912411 -145 ATTTTGGAGTTTTGGCAAAAAGCCTTTTTA 5 95 1 TTTGGCAAAA 0.699609 -93 TGAATGAAAAGTGGGCAAATTTGTCCACTT 7 33 1 GTGGGCAAAT 0.971112 -113 CTCCAGAATATTGGACAAAATAATAATAAA 8 234 0 TTGGACAAAA 0.764178 -67 CGCCGTGAATGCAGGCAAAAACAGCAAAAT 10 50 1 GCAGGCAAAA 0.958869 -251 TCAACCAAGTGCGGTCAAAACAAACGTGAT 11 17 1 GCGGTCAAAA 0.983676 -49 AATAAAAAGTGCGGTCAAAATCACGTTTGT 11 36 0 GCGGTCAAAA 0.983676 -30 ACCGATGTTTTTGGGCAAATGTAATTTGCC 13 58 1 TTGGGCAAAT 0.904623 -38 TATCGATTTTGTAGGCAAATTACATTTGCC 13 71 0 GTAGGCAAAT 0.868757 -25 ********** Masking position 7 Map Score: 10.2454 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 305 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 TGTTGTAGCGAGTGAGATAACCTCTCATAT 1 49 0 AGTGAGATAA 0.767451 -124 CACACAAAATAGTGATATAATTTTTTAGTC 1 129 1 AGTGATATAA 0.822538 -44 TGCAAACTAAGGAGATAAAAG 4 67 1 GGAGATAAAA 0.868922 -11 AATCGTTTACATTGATAAAAAACAGGAGTC 6 185 1 ATTGATAAAA 0.912684 -23 TCAGAATTGAATAGATAAAACAAAAGTGGA 7 56 0 ATAGATAAAA 0.95222 -90 CCATTTTCATAGAGAGAAAAAA 7 134 1 AGAGAGAAAA 0.957685 -12 AGCGGATAAGAGAGATAAAATCAAAATATC 8 120 0 AGAGATAAAA 0.9695 -181 TACATATATAGAGAAAACCTTTATATA 8 284 0 ATAGAGAAAA 0.934176 -17 TCCGAATAGATAAATTGTAGGGGCG 13 6 1 ATAGATAAAT 0.736998 -90 TGCCTACAAAATCGATAAAAAT 13 84 1 ATCGATAAAA 0.85981 -12 ********** Masking position 5 Map Score: 9.29642 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 93 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 TAATCTGAAATAACTTAAATTTTAACCGCACT 5 34 1 TACTTAATTT 0.957579 -154 ATAATCTATAAATCTTATATTTTGATCATAAA 6 26 1 AACTTAATTT 0.753419 -182 GCTTTCAATTTATCGTAAATTATTTATGATCA 6 48 0 TACGTAATTA 0.842775 -160 TATCTTATCTTATCTTATCTTA 8 1 1 TACTTACTTA 0.963913 -300 TATCTTATCTTATCTTATCTTATCTTATCTTA 8 16 1 TACTTACTTA 0.963913 -285 TATCTTATCTTATCTTATCTTTTTCATTGTTC 8 31 1 TACTTACTTT 0.957425 -270 AATCAAAATATCCCTTATCTTAAAATCAAAAA 8 100 0 TCCTTACTTA 0.911164 -201 ACCAAATATATAGCTAACATTAGAGTAATTTT 8 198 0 TACTAAATTA 0.784044 -103 GGAAAATTAATACCTTAAACTATATAAAGGTT 8 264 1 TACTTAACTA 0.842775 -37 CTATTTGCATTACCTTAAATTTATTAACCCAA 9 36 1 TACTTAATTT 0.96 -23 ACCTTTATTTTCCCTTAGATTTGTATAGAATA 10 248 1 TCCTTAATTT 0.902242 -53 ** **** **** Masking position 7 Map Score: 11.3297 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 29 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 AATGAAGCCACGCCGCTATAGGAACTTTCT 2 24 1 CGCCGCTATA 0.969243 -153 GTGAATAATACGCCATAATTGGCACCAAAT 2 69 1 CGCCATAATT 0.840172 -108 CCGCACTTCACGACGCTATTTGAGAAGTGC 5 61 0 CGACGCTATT 0.841834 -127 TGTATAATTGCGCCACCATTTTCATAGAGA 7 119 1 CGCCACCATT 0.966171 -27 AAAGCGGTATCGCCGTGAATGCAGGCAAAA 10 40 1 CGCCGTGAAT 0.916471 -261 ATTTATACATCGCCACGATAATTTCGTGGC 10 148 1 CGCCACGATA 0.983277 -153 CATAAAAAACCGCCACGAAATTATCGTGGC 10 159 0 CGCCACGAAA 0.962376 -142 ********** Masking position 8 Map Score: 2.94859 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 144 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 AGAGCTTGTTTATCTGCATTTTTTCAGTATA 2 110 0 TATCTGCATT 0.793615 -67 AAGAAATTGTTTTTTGAATAATCTGAAATAA 5 16 1 TTTTTGAATA 0.867503 -172 AGTCGCCCTATTTTTGCATATTTTTGAAATT 5 127 0 TTTTTGCATT 0.960151 -61 GGTTTGCCGATTATTGCATAAATATCCTTAA 7 87 0 TTATTGCATA 0.771788 -59 TTATCCGCTATTTTAGTATATTATGATTTTT 8 141 1 TTTTAGTATT 0.56994 -160 GGGTATAGAGTATTTGTATGAAAATTACTCT 8 178 1 TATTTGTATA 0.865466 -123 AGATTTCTTCTATTTGCATTACCTTAAATTT 9 27 1 TATTTGCATA 0.942709 -32 TGCGGTAAGTTTTTTGAATGTTTAGCTTACC 10 109 0 TTTTTGAATT 0.867952 -192 CTTACCGCACTTTGTGCATTTATACATCGCC 10 131 1 TTTGTGCATT 0.849163 -170 CCGCACTTTTTATTTGTATCAACT 11 52 1 TATTTGTATA 0.865466 -14 ********* * Masking position 8 Map Score: 2.85864 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 295 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 ATTATCATATCCATTGTTTAA 3 11 0 TTATCATATC 0.925879 -11 CATTTATTAGATATCCTATCAATCAAGGAA 4 39 0 ATATCCTATC 0.936798 -39 ATTTTGCTTATTTTCTTATTTTGTGACAAA 6 115 1 TTTTCTTATT 0.698709 -93 TATCTTATCTTATCTTATCTTATCTTATC 8 10 1 TTATCTTATC 0.976246 -291 TTATCTTATCTTATCTTATCTTATCTTATC 8 20 1 TTATCTTATC 0.976246 -281 TTATCTTATCTTATCTTATCTTTTTCATTG 8 30 1 TTATCTTATC 0.976246 -271 AAACAGCAAAATTTCCTATCAAATGGGAGC 10 68 1 ATTTCCTATC 0.865737 -233 ********** Masking position 8 Map Score: 7.01909 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 31 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 TTTATTTTATTGAAAATCACCATTCTTACCACA 1 100 1 TAAACACCAT 0.601093 -73 GAAAAACCTCAAAATGAAGCCACGCCGCTATAG 2 12 1 AAATAGCCAC 0.59972 -165 CGCGTGAGTGAATAATACGCCATAATTGGCACC 2 62 1 ATAACGCCAT 0.964658 -115 ATTTTTTCAGTATAATTCGCAACCTATTTGGTG 2 91 0 TTAACGCAAC 0.825041 -86 AAACTCCAAAATAAAACCGCACTTCACGACGCT 5 74 0 AAAACGCACT 0.757854 -114 AAAAATAAAAACTAAGTCGCCCTATTTTTGCAT 5 139 0 ATAACGCCCT 0.944738 -49 CAAACCCTGTATAATTGCGCCACCATTTTCATA 7 112 1 AAATCGCCAC 0.9449 -34 TTTGTGCATTTATACATCGCCACGATAATTTCG 10 141 1 TTACCGCCAC 0.877325 -160 AACTTGCCATAAAAAACCGCCACGAAATTATCG 10 163 0 AAAACGCCAC 0.984049 -138 AAAAGATTGTAAAAACTTGCCATAAAAAACCGC 10 176 0 AAAATGCCAT 0.739162 -125 ATCAGGCGAATGTAATTCGCCCCTACAATTTAT 13 20 0 TTAACGCCCC 0.950424 -76 * *** ****** Masking position 4 Map Score: 3.02871 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 474 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 11 AACCTGTTGCTAAAAAGTATTGTTGTAGCGA 1 68 0 TAAAAAGTTT 0.741694 -105 TCTCAATAATTAACAAGGAAATCATT 1 157 1 TAACAAGGAA 0.915507 -16 TTAACAAGAAATTGTTTTTTGA 5 2 1 TAACAAGAAT 0.8898 -186 TTGAAATTTATAAAAAGGCTTTTTGCCAAAA 5 104 0 TAAAAAGGTT 0.948877 -84 TTATTATGGGTAACAAGGATTCTTTTTA 5 170 1 TAACAAGGTT 0.979371 -18 TTATAGATTATAACAAGGAAAAAGTT 6 6 0 TAACAAGGAA 0.915507 -202 CCTTAAACTATATAAAGGTTTTCTCTATATA 8 276 1 TATAAAGGTT 0.768848 -25 CTATAATCCCTAACAAGAGTTATACAGTTGT 12 38 1 TAACAAGATT 0.928332 -24 ******** ** Masking position 6 Map Score: 4.11684 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 48 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 ********** No masking Map Score: 5.84309e-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: 5.84309e-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: 5.84309e-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