AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -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 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #2 HI0205 292 H. influenzae predicted coding region HI0205 #3 HI0206 22 5'-nucleotidase, putative #4 HI0207 284 shikimic acid kinase I (aroK) #5 HI0604 300 adenylate cyclase (cyaA) #6 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #7 HI0658 160 ABC transporter, ATP-binding protein #8 HI0660 269 H. influenzae predicted coding region HI0660 #9 HI0661 300 hemoglobin-binding protein #10 HI0967 25 H. influenzae predicted coding region HI0967 #11 HI0970 57 3-dehydroquinase (aroQ) #12 HI1587 300 DNA-binding protein H-NS (hns) #13 HI1588 69 formyltetrahydrofolate deformylase (purU) Motif number 1 GTCTATATATACAGAGAAAAAAGTAAGCTATATTCTCAAATCAC 2 61 0 AAAAAAAATT 0.959808 -232 CTCTGTATATATAGACAAAAAGCCTGCGAATTTTATACTTTTCA 2 89 1 AAAAAAAATT 0.959808 -204 ATATCGTAAAACAAAATAAATTGTGAATGATAATTAAAAGGAAT 2 171 0 AATAAATATT 0.687704 -122 CCTAGGACTAATAACAAAAATAGCGCGTTAAATACGCGCTATTT 4 29 0 AAAAAATAAA 0.897618 -256 TAAATATGGAATAGTTAAAATTCTTAATCATCTATGAAGTCTTC 4 76 0 AAAAAATATA 0.954046 -209 TAATTAAATTAAAAGTGAAATAAAATTCGATCATTTCTAATGAA 4 240 0 AAGAAATATT 0.897405 -45 CTTTGCGTTGATAAGAAAAATATCAAGCTATCCACTAATAATAG 5 51 1 AAAAAATATA 0.954046 -250 CTATCCACTAATAATAGAAAATATAGATTTTTATATCGGCAGAA 5 78 1 AAGAAAATTT 0.678319 -223 TTACCTATCAACAATCAAAATGACTTTTTTACCTAAGAGTGGTA 5 157 0 AAAAAATTAT 0.755072 -144 TTGATTGTTGATAGGTAAAATTTATAGTATTTTTCGAAAAATTG 5 183 1 AAAAAATTTT 0.921663 -118 TAGGGAGTATAAATGCAAAAAAATGTGACATAAATCACAATTTT 5 220 0 AAAAAAAATA 0.935574 -81 CCCTACCAGAACAACAAAAATTGGCGAACAATTTACCACTTAGG 5 260 0 AAAAAATAAT 0.935139 -41 GACTGTTCCGAGAAAAGAAAAAATATTGCAAAATAGCCTCAAAT 7 109 1 AAGAAAAAAT 0.720996 -52 ACCTATCTAAAATCAAAAGTGCGGTAAATTTTTACCGCACTT 8 9 1 AAAAAAGATT 0.90154 -261 GATCGCAAAAATAGCGAAAATAGCTTGATTTTCAAGGAGATTTT 8 121 0 AAAAAATTTA 0.877371 -149 TCATAAATAGAAACTAAAAATTTGGCGAGATAGTCATTTCAATC 8 175 0 AAAAAATATT 0.971543 -95 GATTACTCCTAAAATAAAAAGAAGTACGCATAGAAAGAATTATG 9 43 1 AAAAAAGATA 0.847872 -258 ATCAAAATCAAGAAATAAAAACTATTCTCATTATTTGCTGTATT 9 217 0 AAAAAAAATT 0.849574 -84 CGACCACCAAAAATCGAAAAAACCAGTATAATGTGCCACACAAA 11 13 1 AAAAAAAAAT 0.909785 -45 TGGATAACGAAGAAGAAAAAAGAAAGGAATAGTTGCCGAAATCA 12 17 0 AAAAAAATAT 0.776557 -284 TTACCGTAAAACAAACAAAATGCCAACAGATTTTATAAAAATTT 12 116 1 AAAAAATATT 0.971543 -185 TAATAAAAATATAAAGAAAATAAACACAAAAAAATATATCTGTT 12 169 1 AAAAAATAAA 0.897618 -132 TTATTTAATAATAGAGAAAATAAAATTTATTGTAAATATCTATT 12 230 0 AAAAAATTTA 0.87737 -71 TGCTATGTTTAGATAAAAAAATAGAACCCATAAAATAGGTTCTA 13 27 0 AAAAAAAATA 0.935574 -43 * * ***** ** * Masking position 10 Map Score: 30.7399 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 369 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 2 CTAAAAGAATATTCTCAAATTCGAAAGTGATTTGAGAATA 2 35 1 ATTTCATAGA 0.816112 -258 TCGCAGGCTTTTTGTCTATATATACAGAGAAAAAAGTAAG 2 78 0 TTTTCATAGA 0.969684 -215 GAATTTTATACTTTTCAAGCAAAATTGCAAGTTTTGTATG 2 116 1 CTTTCAAAAA 0.803877 -177 AATCACCCTATTTTTCAACCTCTATAGGGAATTTATTTTC 4 134 0 TTTTCATAGA 0.979789 -151 TGTTCTTTATCTAATTAAATTAAAAGTGAAATAAA 4 260 0 TTTTCATAAA 0.973883 -25 TACTATAAATTTTACCTATCAACAATCAAAATGACTTTTT 5 172 0 TTTCCAAAAA 0.803574 -129 TAAATCACAATTTTTCGAAAAATACTATAAATTTTACCTA 5 194 0 TTTTCAAAAA 0.967954 -107 ATCTACAATTTATCTAGTAAAAGAGGAAATAAGTATAG 6 46 0 TTTTCAAAAA 0.956965 -28 TATACGTGGCTTTTTTGACTAGAAAATCGATAAAATCGGA 7 66 1 TTTTTAAAGA 0.803379 -95 TTTTCGCTATTTTTGCGATCTAGATCGAAAGATTGAAATG 8 145 1 TTTGCATAAA 0.839232 -125 TAATTAGGCGTTTATCTATCATCATAATGATTACTCCTAA 9 15 1 TTTTCAAAGA 0.974399 -286 ATAGTTTTTATTTCTTGATTTTGATCAAAAATACACTTTT 9 236 1 TTTTTATAAA 0.804986 -65 TTATAAGTATTTTTTCAGAGTGGATAACGAAGAAGAAAAA 12 41 0 TTTTCGTAGA 0.860104 -260 TTATAAAAATTTTATAAACTTTAATAAAAATATAAAGAAA 12 148 1 TTTTAATAAA 0.700288 -153 TAAATTTTATTTTCTCTATTATTAAATAAATTTTCCCACA 12 245 1 TTTTCAAAAA 0.554564 -56 TTTTTCTATTTGAAACTAGAACCTATTTTA 13 1 1 TTTTCATAGA 0.979624 -69 *** ** * * * ** Masking position 14 Map Score: 17.9356 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 99 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 GTGATTTGAGAATATAGCTTACTTTTTTCT 2 61 1 AATATAGCTT 0.741985 -232 TTGTATGCATAAAGTAGGTTGTATTCCTTT 2 149 1 AAAGTAGGTT 0.897111 -144 TTATCAAGCTAAAATACCGCTATACGCGTA 2 248 0 AAAATACCGC 0.81329 -45 AATTGAAAAATAGGCTAAAAATAGCG 4 7 1 AAAATAGGCT 0.892508 -278 AAATAGGCTAAAAATAGCGCGTATTTAACG 4 18 1 AAAATAGCGC 0.926861 -267 ACTAATAACAAAAATAGCGCGTTAAATACG 4 37 0 AAAATAGCGC 0.926861 -248 TAGAGGTTGAAAAATAGGGTGATTTATTGC 4 150 1 AAAATAGGGT 0.9688 -135 GATCTCCCAAAAAATGGGGTAGATTATCGC 4 178 0 AAAATGGGGT 0.918657 -107 AAAGTATTATAAAATACCTTACTCAATATC 5 25 0 AAAATACCTT 0.867343 -276 TTTTATTGCGTAAATAGCTTAATTCTGCCG 5 114 0 TAAATAGCTT 0.604885 -187 AAAATATTGCAAAATAGCCTCAAATTAAGA 7 128 1 AAAATAGCCT 0.903071 -33 TCTAAAATCAAAAGTGCGGTAAATTTTTAC 8 16 1 AAAGTGCGGT 0.66598 -254 TTCTTAAGAAAAAGTGCGGTAAAAATTTAC 8 34 0 AAAGTGCGGT 0.66598 -236 AAAAATAGCGAAAATAGCTTGATTTTCAAG 8 129 0 AAAATAGCTT 0.950139 -141 ATGCGTACTTAATGTAGGGTGGGCTTCAGC 9 84 1 AATGTAGGGT 0.706429 -217 TCAGCCCACCAAAATATCTTACGATTGTTT 9 109 1 AAAATATCTT 0.556334 -192 TAGAACCCATAAAATAGGTTCTAGTTTCAA 13 20 0 AAAATAGGTT 0.944391 -50 ********** Masking position 5 Map Score: 18.0264 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 359 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 TACTTAATGTAGGGTGGGCTTCAGCCCACC 9 89 1 AGGGTGGGCT 0.995155 -212 GTAAGATATTTTGGTGGGCTGAAGCCCACC 9 101 0 TTGGTGGGCT 0.992527 -200 CGATTGTTTGATGGTGGGCTGAAGCCCACC 9 130 1 ATGGTGGGCT 0.994773 -171 TAGTAATTGTAGGGTGGGCTTCAGCCCACC 9 142 0 AGGGTGGGCT 0.995155 -159 TTTTCGATTTTTGGTGGTCGAA 11 3 0 TTGGTGGTCG 0.919774 -55 ********** Masking position 5 Map Score: 7.14243 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 18 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 AAATGTTTAATTACTAAAAGAATATTCTCAAATTCG 2 22 1 TTCTAGAATT 0.872354 -271 GGAATTTATTTTCCACGAGAAAGCATCTAAATATGG 4 111 0 TTCAAAAAGT 0.86072 -174 CGCAGTTTATTTTCATTAGAAATGATCGAATTTTAT 4 229 1 TTCAAAAATT 0.930693 -56 ATTCCTTAATAAGTGATATTGAGTAAG 5 2 1 TTCTAAAGTT 0.872353 -299 ATTTATAGTATTTTTCGAAAAATTGTGATTTATGTC 5 202 1 TTTTAAAATT 0.950915 -99 ATTTCCTCTTTTACTAGATAAATTGTAGAT 6 54 1 TTCTAAAATT 0.959258 -20 TATTGACTTGTTATATTATAAATAGTTTTTATTGCG 7 24 1 TTTAAAAATT 0.917008 -137 TACCGCACTTTTTCTTAAGAAAGGATCTATCTTTTA 8 43 1 TTCTAAAAGT 0.915483 -227 GTACTTCTTTTTATTTTAGGAGTAATCATTATGATG 9 34 0 TTTTAGAGTT 0.620095 -267 ACATATTATAGGAGAAAGTATTCTCTCACAA 9 280 0 TTTAAAAAGT 0.835657 -21 ATGCCAACAGATTTTATAAAAATTTTATAAACTTTA 12 135 1 ATTTAAAATT 0.784267 -166 TAAATATCTATTATTAAATAAATGGTCGAAACAGAT 12 206 0 TTTTAAAATT 0.950915 -95 AATAATAGATATTTACAATAAATTTTATTTTCTCTA 12 227 1 ATTAAAAATT 0.674633 -74 ATTTTCTCTATTATTAAATAAATTTTCCCACATTTA 12 253 1 TTTTAAAATT 0.950915 -48 ** ** * **** * Masking position 8 Map Score: 10.8073 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 163 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 TATTTTTCCCTAATCTAAATGGTAAA 1 10 0 TTTTCCTATA 0.910425 -17 TAAAGTAGGTTGTATTCCTTTTAATTATCATTCACAA 2 158 1 TTTTCTTATA 0.875001 -135 CAATTTATTTTGTTTTACGATATAATACGAGGCATCC 2 192 1 TTTTCGTTTA 0.970256 -101 AATAGGGTGATTTATTGCGATAATCTACCCCATTTTT 4 162 1 TTTTCGTATA 0.984183 -123 TAAGTATAGATATCTTTCGGTAACCTATCAACCACAG 6 18 0 TTTTCGTATA 0.970291 -56 ATAAATAGTTTTTATTGCGTCTTATTATACGTGGCTT 7 41 1 TTTTCGCTTA 0.941428 -120 CTCGGAACAGTCTATTCCGATTTTATCGATTTTCTAG 7 84 0 TTTTCGTTTC 0.941428 -77 GCATTTTGTTTGTTTTACGGTAATCTCCCCAATCACT 12 102 0 TTTTCGTATC 0.968025 -199 AAAAAATATATCTGTTTCGACCATTTATTTAATAATA 12 197 1 TTTTCGCATA 0.968395 -104 * * ** ** * * ** Masking position 6 Map Score: 6.6924 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 31 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 CGTATTTAACGCGCTATTTTTGTTATTAGTCC 4 37 1 GGTATTTTTG 0.427112 -248 CTTTCTATCTTCTGCATTTTTACGCAGTTTAT 4 207 1 TTCATTTTTA 0.735376 -78 AGTGGATAGCTTGATATTTTTCTTATCAACGC 5 55 0 TGTATTTTTC 0.44088 -246 AAATCTATATTTTCTATTATTAGTGGATAGCT 5 76 0 TTTATTATTA 0.64673 -225 TAATAGAAAATATAGATTTTTATATCGGCAGA 5 89 1 TTGATTTTTA 0.90121 -212 AAAAAAGTCATTTTGATTGTTGATAGGTAAAA 5 171 1 TTGATTGTTG 0.667424 -130 TTTCGAAAAATTGTGATTTATGTCACATTTTT 5 214 1 TGGATTTATG 0.560898 -87 GTCACATTTTTTTGCATTTATACTCCCTAAGT 5 235 1 TTCATTTATA 0.334382 -66 TTTACCGCACTTTTGATTTTAGATAGGT 8 7 0 TTGATTTTAG 0.692991 -263 CAAGCTATTTTCGCTATTTTTGCGATCTAGAT 8 138 1 TGTATTTTTG 0.881162 -132 AAATTTTTAGTTTCTATTTATGATTACACATC 8 196 1 TTTATTTATG 0.772418 -74 ACCAATAAGTTATTGATTTTTGATGTGTAATC 8 217 0 TTGATTTTTG 0.947067 -53 TGCGTACTTCTTTTTATTTTAGGAGTAATCAT 9 41 0 TTTATTTTAG 0.703144 -260 AGTTTTTATTTCTTGATTTTGATCAAAAATAC 9 238 1 TTGATTTTGA 0.491729 -63 CAATACTAAAAGTGTATTTTTGATCAAAATCA 9 251 0 ATTATTTTTG 0.560186 -50 ATACTGGTTTTTTCGATTTTTGGTGGTCGAA 11 10 0 TTGATTTTTG 0.947067 -48 GTTTATTTTCTTTATATTTTTATTAAAGTTTA 12 162 0 TTTATTTTTA 0.905426 -139 TCGAAACAGATATATTTTTTTGTGTTTATTTT 12 185 0 TTTTTTTTTG 0.691926 -116 TTATTGTAAATATCTATTATTAAATAAATGGT 12 216 0 TTTATTATTA 0.646729 -85 AATTTTATTTTCTCTATTATTAAATAAATTTT 12 247 1 TTTATTATTA 0.64673 -54 TTTTATGGGTTCTATTTTTTTATCTAAACATA 13 36 1 TTTTTTTTTA 0.533863 -34 * * ******** Masking position 7 Map Score: 10.8943 Number of sites scoring better than the average of aligned sites = 862 Number in coding regions = 622 Number in noncoding regions = 240 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 8 TAAAAATGCAGAAGATAGAAAGATCTCCCA 4 199 0 GAAGATAGAA 0.717994 -86 AATACTTTGCGTTGATAAGAAAAATATCAA 5 47 1 GTTGATAAGA 0.811092 -254 CATTTTGATTGTTGATAGGTAAAATTTATA 5 179 1 GTTGATAGGT 0.973104 -122 TTTTCCTGTGGTTGATAGGTTACCGAAAGA 6 13 1 GTTGATAGGT 0.973104 -61 ACTTTTGATTTTAGATAGGT 8 1 0 TTAGATAGGT 0.782801 -269 ATTGAAATAAGTAGATAAATAGGATAAATT 8 250 1 GTAGATAAAT 0.785866 -20 TAATCATTATGATGATAGATAAACGCCTAA 9 18 0 GATGATAGAT 0.884 -283 ********** Masking position 5 Map Score: 1.05147 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 41 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ********** No masking Map Score: -4.47399e-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 10 ********** No masking Map Score: -4.47399e-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: -4.47399e-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