AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_hinf_reg_100.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 HI0207 284 shikimic acid kinase I (aroK) #3 HI0604 300 adenylate cyclase (cyaA) #4 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #5 HI0658 160 ABC transporter, ATP-binding protein #6 HI0967 25 H. influenzae predicted coding region HI0967 #7 HI0970 57 3-dehydroquinase (aroQ) #8 HI1587 300 DNA-binding protein H-NS (hns) #9 HI1588 69 formyltetrahydrofolate deformylase (purU) Motif number 1 ATACGCGCTATTTTTAGCCTATTTTTCAATT 2 6 0 TTTTTATTTT 0.962512 -279 AACTATTCCATATTTAGATGCTTTCTCGTGGAAAAT 2 104 1 TATTTATTTT 0.735675 -181 AAATCACCCTATTTTTCAACCTCTATAGGGAATTTA 2 139 0 ATTTTTTCTT 0.915837 -146 TCTACCCCATTTTTTGGGAGATCTTTCTATCTTCTG 2 185 1 TTTTTGTCTT 0.766456 -100 ATCTTCTGCATTTTTACGCAGTTTATTTTCATTAGA 2 213 1 TTTTTATTTT 0.962512 -72 AAATGATCGAATTTTATTTCACTTTTAATTTAATTA 2 248 1 ATTTTACTTT 0.936227 -37 TGAGTAAGGTATTTTATAATACTTTGCGTTGATAAG 3 30 1 ATTTTACTTG 0.711114 -271 TGATAGGTAAAATTTATAGTATTTTTCGAAAAATTG 3 191 1 AATTTATTTT 0.861302 -110 TTTATGTCACATTTTTTTGCATTTATACTCCCTAAG 3 230 1 ATTTTTTTTT 0.949111 -71 TTGTTCGCCAATTTTTGTTGTTCTGGTAGGGACACC 3 273 1 ATTTTTTCTG 0.645967 -28 GACTTGTTATATTATAAATAGTTTTTATTGCGTCTT 5 28 1 ATTATATTTT 0.927465 -133 ATTGCGTCTTATTATACGTGGCTTTTTTGACTAGAA 5 54 1 ATTATACTTT 0.766176 -107 GTCTATTCCGATTTTATCGATTTTCTAGTCAAAAAA 5 76 0 ATTTTATTTT 0.982843 -85 ATTTGAGGCTATTTTGCAATATTTTTTCTTTTCTCG 5 117 0 ATTTTGTTTT 0.926201 -44 TGTGTGGCACATTATACTGGTTTTTTCGATTTTTGG 7 19 0 ATTATATTTT 0.927465 -39 TTTTAATCCTTTTTGTGTGGCACATT 7 42 0 TTTTAATTTT 0.807115 -16 AGGCGCAATTATTATAAGTATTTTTTCAGAGTGGAT 8 56 0 ATTATATTTT 0.927465 -245 GTTTATAAAATTTTTATAAAATCTGTTGGCATTTTG 8 131 0 TTTTTATCTT 0.937423 -170 TTCTTTATATTTTTATTAAAGTTTATAAAATTTTTA 8 151 0 TTTTATTTTT 0.576686 -150 AAACAGATATATTTTTTTGTGTTTATTTTCTTTATA 8 178 0 ATTTTTTTTT 0.949111 -123 TTTACAATAAATTTTATTTTCTCTATTATTAAATAA 8 238 1 ATTTTATCTT 0.97095 -63 ATTTTCCCACATTTAATGTTATTTATTGAGGTTTAT 8 274 1 ATTTAATTTT 0.903251 -27 ACTAGAACCTATTTTATGGGTTCTATTTTTTTATCT 9 25 1 ATTTTATCTT 0.97095 -45 ****** *** * Masking position 3 Map Score: 33.2313 Number of sites scoring better than the average of aligned sites = 871 Number in coding regions = 558 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 2 TATTTTTCCCTAATCTAAATGG 1 15 0 TATTTTTCTA 0.776264 -12 ATTTAACGCGCTATTTTTGTTATTAGTCCTAG 2 40 1 CTATTTTTTA 0.783019 -245 TTTACGCAGTTTATTTTCATTAGAAATGATCG 2 225 1 TTATTTTTTA 0.913905 -60 TGATCGAATTTTATTTCACTTTTAATTTAATT 2 251 1 TTATTTCTTT 0.902104 -34 GGATAGCTTGATATTTTTCTTATCAACGCAAA 3 52 0 ATATTTTTTA 0.475969 -249 TAAAAATCTATATTTTCTATTATTAGTGGATA 3 79 0 TATTTTCTTA 0.73809 -222 ATCAAAATGACTTTTTTACCTAAGAGTGGTAG 3 156 0 CTTTTTTCTA 0.8532 -145 ATGTCACATTTTTTTGCATTTATACTCCCTAA 3 233 1 TTTTTGCTTA 0.741395 -68 ATATCTATACTTATTTCCTCTTTTACTAGATA 4 42 1 TTATTTCCTT 0.930564 -32 GATATACCCGTTATATTGACTTGTTATATTAT 5 11 1 TTATATTCTT 0.602183 -150 TAAATAGTTTTTATTGCGTCTTATTATACGTG 5 42 1 TTATTGCCTT 0.734494 -119 TTATACGTGGCTTTTTTGACTAGAAAATCGAT 5 65 1 CTTTTTTCTA 0.8532 -96 TCTATTCCGATTTTATCGATTTTCTAGTCAAA 5 79 0 TTTTATCTTT 0.576597 -82 TATTTTGCAATATTTTTTCTTTTCTCGGAACA 5 112 0 TATTTTTTTT 0.636742 -49 ATTATACTGGTTTTTTCGATTTTTGGTGGTCG 7 13 0 TTTTTTCTTT 0.910752 -45 TATTCCTTTCTTTTTTCTTCTTCGTTATCCAC 8 30 1 TTTTTTCCTT 0.936873 -271 TTTTTTGTGTTTATTTTCTTTATATTTTTATT 8 170 0 TTATTTTTTA 0.913906 -131 ACAATAAATTTTATTTTCTCTATTATTAAATA 8 241 1 TTATTTTCTA 0.939165 -60 ATGGGTTCTATTTTTTTATCTAAACATAGCAC 9 40 1 TTTTTTTCTA 0.94474 -30 ******* *** Masking position 4 Map Score: 16.1513 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 625 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 3 ATGGGGTAGATTATCGCAATAAATCACCCTATT 2 162 0 TTATCGCAAA 0.905244 -123 AAATTCGATCATTTCTAATGAAAATAAACTGCG 2 229 0 ATTTCTAAAA 0.648769 -56 TGTTCTTTATCTAATTAAATTAAAAGTGA 2 266 0 TTATCTAAAA 0.974028 -19 ACTATAAATTTTACCTATCAACAATCAAAATGA 3 178 0 TTACCTATAA 0.727269 -123 AAATCACAATTTTTCGAAAAATACTATAAATTT 3 200 0 TTTTCGAAAA 0.927132 -101 GGTTGATAGGTTACCGAAAGATATCTATACTTA 4 22 1 TTACCGAAAA 0.932955 -52 ATCTACAATTTATCTAGTAAAAGAGGAAATAA 4 52 0 TTATCTAGAA 0.954491 -22 ATTTTATCGATTTTCTAGTCAAAAAAGCCACGT 5 69 0 TTTTCTAGAA 0.906646 -92 ATATTTTTTCTTTTCTCGGAACAGTCTATTCCG 5 102 0 TTTTCTCGAA 0.770709 -59 ATTGGGGAGATTACCGTAAAACAAACAAAATGC 8 106 1 TTACCGTAAA 0.638726 -195 TTTCGACCATTTATTTAATAATAGATATTTACA 8 211 1 TTATTTAAAA 0.826064 -90 GTGGGAAAATTTATTTAATAATAGAGAAAATAA 8 251 0 TTATTTAAAA 0.826064 -50 TTCTATTTTTTTATCTAAACATAGCACACAACA 9 45 1 TTATCTAAAA 0.974049 -25 ******** * * Masking position 11 Map Score: 9.89945 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 205 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 TACCATTTAGATTAGGGAAAAATA 1 13 1 ATTAGGGAAA 0.923901 -14 TTTTAATTTAATTAGATAAAGAACA 2 270 1 ATTAGATAAA 0.980316 -15 TCCTACCACTCTTAGGTAAAAAAGTCATTT 3 154 1 CTTAGGTAAA 0.868047 -147 TTCCTCTTTTACTAGATAAATTGTAGAT 4 56 1 ACTAGATAAA 0.931016 -18 AGTTGCCGAAATCAAATAAA 8 1 0 ATCAAATAAA 0.79556 -300 AATATCTATTATTAAATAAATGGTCGAAAC 8 210 0 ATTAAATAAA 0.942991 -91 TTTATTTAATAATAGAGAAAATAAAATTTA 8 245 0 AATAGAGAAA 0.816576 -56 TTTCTCTATTATTAAATAAATTTTCCCACA 8 255 1 ATTAAATAAA 0.942991 -46 GTGTGCTATGTTTAGATAAAAAAATAGAAC 9 44 0 TTTAGATAAA 0.890643 -26 ********** Masking position 4 Map Score: 6.01086 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 341 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 GGTGATTTATTGCGATAATCTACCCCATTT 2 167 1 TGCGATAATC 0.856046 -118 TGAAATAAAATTCGATCATTTCTAATGAAA 2 239 0 TTCGATCATT 0.922737 -46 TGGTAAATTGTTCGCCAATTTTTGTTGTTC 3 266 1 TTCGCCAATT 0.896973 -35 ATAGATATCTTTCGGTAACCTATCAACCAC 4 20 0 TTCGGTAACC 0.958116 -54 TTCGACCACCAAAAATCGAA 7 1 1 TTCGACCACC 0.96716 -57 TTTATTTGATTTCGGCAACTATTCCTTTCT 8 11 1 TTCGGCAACT 0.958116 -290 TTGTTTGTTTTACGGTAATCTCCCCAATCA 8 104 0 TACGGTAATC 0.82892 -197 ATATATCTGTTTCGACCATTTATTTAATAA 8 202 1 TTCGACCATT 0.949857 -99 ********** Masking position 8 Map Score: 3.34832 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 105 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 CCTAGGACTAATAACAAAAATAGCGCGTTA 2 43 0 ATAACAAAAA 0.69222 -242 ATAGAAAGATCTCCCAAAAAATGGGGTAGA 2 185 0 CTCCCAAAAA 0.753223 -100 TACCTATCAACAATCAAAATGACTTTTTTA 3 170 0 CAATCAAAAT 0.715514 -131 CCCTACCAGAACAACAAAAATTGGCGAACA 3 274 0 ACAACAAAAA 0.776732 -27 CTGTTCCGAGAAAAGAAAAAATATTGCAAA 5 111 1 AAAAGAAAAA 0.540355 -50 TTCGACCACCAAAAATCGAAAAAACC 7 7 1 CACCAAAAAT 0.518405 -51 TATAATGTGCCACACAAAAAGGATTAAAA 7 39 1 CACACAAAAA 0.966227 -19 TACCGTAAAACAAACAAAATGCCAACAGAT 8 117 1 CAAACAAAAT 0.947019 -184 AAAGAAAATAAACACAAAAAAATATATCTG 8 181 1 AACACAAAAA 0.928314 -120 AATAATAGAGAAAATAAAATTTATTGTAAA 8 238 0 AAAATAAAAT 0.583101 -63 AAAAATAGAACCCATAAAATAGGTTCTAGT 9 25 0 CCCATAAAAT 0.680159 -45 CTAAACATAGCACACAACATT 9 59 1 CACACAACAT 0.830833 -11 ********** Masking position 6 Map Score: 1.09848 Number of sites scoring better than the average of aligned sites = 1101 Number in coding regions = 907 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 7 GATTATCGCAATAAATCACCCTATTTTTCA 2 157 0 ATAAATCACC 0.9086 -128 ATTTAATTAGATAAAGAACA 2 275 1 ATAAAGAACA 0.944091 -10 AAAATGTGACATAAATCACAATTTTTCGAA 3 215 0 ATAAATCACA 0.969977 -86 TCGGTAACCTATCAACCACAGGAAAATA 4 9 0 ATCAACCACA 0.914758 -65 TAATAAAAATATAAAGAAAATAAACACAAA 8 169 1 ATAAAGAAAA 0.68655 -132 ATAAACCTCAATAAATAACATTAAATGTGG 8 280 0 ATAAATAACA 0.939913 -21 AATAAACCTCAATAAATAACA 8 290 0 ATAAACCTCA 0.878648 -11 ********** Masking position 5 Map Score: 2.40577 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 164 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GTTATTAGTCCTAGGTTTGAAGACTTCATA 2 58 1 CTAGGTTTGA 0.902585 -227 CGCAATAAAACTAGGTACTATCCTACCACT 3 134 1 CTAGGTACTA 0.923726 -167 TATATTATAAATAGTTTTTATTGCGTCTTA 5 35 1 ATAGTTTTTA 0.825434 -126 TTTTCTACATAGGTCTTAATTTGAGGCT 5 143 0 ATAGGTCTTA 0.932291 -18 AACCCATAAAATAGGTTCTAGTTTCAAATA 9 17 0 ATAGGTTCTA 0.979617 -53 AACCTATTTTATGGGTTCTATTTTTTTATC 9 30 1 ATGGGTTCTA 0.94616 -40 ********** Masking position 6 Map Score: 0.146553 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 26 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 ********** No masking Map Score: 3.4912e-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: 3.4912e-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: 3.4912e-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