AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00580_hinf_reg_300.orf -o00580_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 HI0645 54 lysophospholipase L2 (pldB) #2 HI0646 158 aspartate-semialdehyde dehydrogenase (asd) #3 HI0647 277 transport protein, putative #4 HI0648 241 modulator of drug activity B (mdaB) #5 HI0652 62 3-deoxy-d-manno-octulosonic-acid transferase (kdtA) #6 HI0686 292 glycerol-3-phosphatase transporter (glpT) #7 HI0687 99 conserved hypothetical protein #8 HI0688 94 H. influenzae predicted coding region HI0688 Motif number 1 TACGCCCTTTGTAGTGAAAGTAAAAT 1 1 0 GTATAAAAAT 0.820725 -54 AAAGTGTGGTTAATTTAAAAGAAAATTTAATTTAAT 2 21 0 TAATAAAAAT 0.874053 -138 TTTCGCGAAAGAAATTAAATAAAAAAGTGTGGTTAA 2 44 0 GAATAAAAAA 0.961715 -115 GCGAAAGATCAATTTTCATTAAAAATACTTGATTTT 2 74 1 AATTAAAAAT 0.802971 -85 GAATCTTAACGAAATAAACAAAAAATCCATCTTCGT 3 31 0 GAATAAAAAT 0.981653 -247 GCTTGGGGTTGAATTTTGCATAAAATAACCATTCTT 3 116 1 GAATGAAAAT 0.975642 -162 TTTAAAATAAAAAATCGGCAGAAAATTTCTTGCCGA 4 17 0 AAATGAAAAT 0.973632 -225 AAAATTGGTGGAAATCGAACGAAAAATGACCGCACT 4 53 0 GAATAAAAAA 0.961715 -189 CTGGAATTGAAAATTCGGTAAAAAATTGGTGGAAAT 4 74 0 AAATGAAAAT 0.973507 -168 TATACTTTTAAAAATTAACGTAAAAAGGCATA 4 220 1 AAATAAAAAA 0.958602 -22 AGTATAGCAAAAAAAGGATTGAAAAT 5 1 0 AAAAAAAAAT 0.924616 -62 CCCGATTCCCAAAATGTAAGAAAAAATAATATAAAA 6 19 1 AAATAAAAAA 0.958603 -274 TCATTGTAGGGAAGTGCGGCCAAAATTAACAACATT 6 62 1 GAATGAAAAT 0.975645 -231 ATAAGAAAGTAAAAAAAATCAAAAATGTGAAGTGTT 6 177 0 AAAAAAAAAT 0.924616 -116 GCGAATCATAAAAGAAAATAAAAAATAAGAAAGTAA 6 201 0 AAAAAAAAAT 0.924616 -92 ACATAATTAAAAAGTTGGAGAAAAAATT 6 275 1 AAATGAAAAA 0.945466 -18 *** * * ***** Masking position 12 Map Score: 25.8788 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 380 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 2 ATTTAATTTAATCACTCTTTTT 2 2 0 ATCACCTTTT 0.802102 -157 TTTTAAATTAACCACACTTTTTTATTTAATT 2 37 1 ACCACCTTTT 0.932539 -122 TTCGCGAAAGATCAATTTTCATTAAAAATAC 2 71 1 ATCAATTTCA 0.32917 -88 TTCAGAATCTACCAAGTTTTTTGGGCAACCA 3 68 1 ACCAATTTTT 0.94187 -210 TCTTTAATTTATCACCTTTCTTGCGAAAATT 3 187 0 ATCACTTTCT 0.791161 -91 AAAATTTCTTGCCGATTTTTA 4 1 0 GCCGATTTTA 0.856664 -241 GAAATTTTCTGCCGATTTTTTATTTTAAAAG 4 24 1 GCCGATTTTT 0.96274 -218 ACGAAAAATGACCGCACTTTTAAAATAAAAA 4 40 0 ACCGCCTTTT 0.961068 -202 TTCGATTTCCACCAATTTTTTACCGAATTTT 4 70 1 ACCAATTTTT 0.94187 -172 CCAATTTTTTACCGAATTTTCAATTCCAGCT 4 81 1 ACCGATTTTC 0.878421 -161 ATATTTGTCTGCCACGTTATTTCTAGACTAT 4 192 0 GCCACTTATT 0.661639 -50 TGCTATACTAGCCGAAATTTTTTTAAGTATA 5 28 1 GCCGAATTTT 0.702855 -35 TTTAAGTATAACCGAATTTCATTT 5 49 1 ACCGATTTCA 0.749284 -14 GTTAATTTTGGCCGCACTTCCCTACAATGAT 6 61 0 GCCGCCTTCC 0.710796 -232 ATATCACAAAATCGCTTTCTTTTACACTCAA 6 98 0 ATCGCTTCTT 0.629548 -195 TGTGAAACACTTCACATTTTTGATTTTTTTT 6 172 1 TTCACTTTTT 0.634079 -121 AATTTTTTCTCCAACTTTTTAATTATGTGT 6 273 0 TCCAATTTTT 0.767948 -20 CAATTTGCCCACCGCCTTTTTTAAGCTAA 7 9 0 ACCGCTTTTT 0.981015 -91 AAATTGCTTAGTCGCCTTTTTTGTAACTATC 7 34 1 GTCGCTTTTT 0.931173 -66 ***** ***** Masking position 8 Map Score: 20.7667 Number of sites scoring better than the average of aligned sites = 2247 Number in coding regions = 1631 Number in noncoding regions = 616 Number of orfs with sites within 600 bp upstream = 398 Fraction of orfs with sites within 600 bp upstream = 0.0639255 Motif number 3 ATTTAATTTCTTTCGCGAAAGATCAATTTT 2 60 1 TTTCGCGAAA 0.49971 -99 TAAGCCTTGGTTGCCCAAAAAACTTGGTAG 3 76 0 TTGCCCAAAA 0.948713 -202 TGAAATTTTATAGAGCGAAAGAATGGTTAT 3 140 0 TAGAGCGAAA 0.721056 -138 TCTACTCAATTTTCGCAAGAAAGGTGATAA 3 180 1 TTTCGCAAGA 0.867968 -98 CCACCAATTTTTTACCGAATTTTCAATTCC 4 78 1 TTTACCGAAT 0.81581 -164 TTTCGGCTAGTATAGCAAAAAAAGGATTGA 5 15 0 TATAGCAAAA 0.848548 -48 TTTACCCCCGATTCCCAAAATGTAAGAAAA 6 13 1 ATTCCCAAAA 0.875307 -280 TTGTGATCAATATCACAAAATCGCTTTCTT 6 108 0 TATCACAAAA 0.799834 -185 TTTACACCGTTTGAGCGAATGCGAAAATTA 6 138 0 TTGAGCGAAT 0.783138 -155 ATGTGAAGTGTTTCACAAATCTTTACACCG 6 159 0 TTTCACAAAT 0.851038 -134 TTCTTTTATGATTCGCAAATCCCTTACTGT 6 221 1 ATTCGCAAAT 0.776113 -72 TTTTACTTTTCCCAAAAATGATACTTA 7 83 0 TTTCCCAAAA 0.95706 -17 ********** Masking position 8 Map Score: 7.94549 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 563 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 GCGTAGTAAATACGCCCTTTGTAGTGAAAG 1 17 0 TACGCCCTTT 0.982659 -38 GCGTATTTACTACGCCCTTTTCATTAAAAA 1 32 1 TACGCCCTTT 0.982659 -23 TATGCCTTTTTACGTTAATT 4 232 0 TATGCCTTTT 0.949869 -10 CTACAATGATTACACTTTTTATATTATTTT 6 41 0 TACACTTTTT 0.833737 -252 CACAAATCTTTACACCGTTTGAGCGAATGC 6 146 0 TACACCGTTT 0.942593 -147 TGTGAAACACTTCACATTTTTGATTTTTTT 6 172 1 TTCACATTTT 0.724553 -121 GTCATCTAAATTTACCCTTTTGAAACAGTA 6 245 0 TTTACCCTTT 0.883275 -48 AAATTGCTTAGTCGCCTTTTTTGTAACTAT 7 34 1 GTCGCCTTTT 0.876324 -66 GATATTTAACTATACCTATTCCACCAACAT 8 26 0 TATACCTATT 0.698799 -69 ********** Masking position 9 Map Score: 5.52966 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 384 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 ACGCCCTTTGTAGTGAAAGTAAAAT 1 4 0 TAGTGAAAAA 0.706371 -51 TACGCCCTTTTCATTAAAAAATT 1 42 1 TCATTAAAAT 0.660071 -13 AAAAAGAGTGATTAAATTAAATTTTCTTTT 2 9 1 TGATTAAAAA 0.906295 -150 TAAAAAAGTGTGGTTAATTTAAAAGAAAATTT 2 29 0 TGGTTAATAA 0.628759 -130 TTCGCGAAAGAAATTAAATAAAAAAGTGTGGT 2 47 0 AAATTAAAAA 0.574067 -112 AGATCAATTTTCATTAAAAATACTTGATTTTS 2 79 1 TCATTAAATA 0.400519 -80 AAGATAGCGTTAGAAAATCAAGTATTTTTAA 2 92 0 TAGAAAAAA 0.182372 -67 GCAAGAAAGGTGATAAATTAAAGACTTGGAAA 3 194 1 TGATAAATAA 0.63962 -84 AATGATAAAAATAAGTCCGACATA 3 264 0 TGATAAAAAA 0.916631 -14 AATTGAAAATTCGGTAAAAAATTGGTGGAAAT 4 74 0 TCGGTAAAAT 0.344681 -168 AATTCGGTTATACTTAAAAAAATTTCGGCTAG 5 35 0 TACTTAAAAA 0.635199 -28 AAAAATAAGAAAGTAAAAAAAATCAAAAATGT 6 185 0 AAGTAAAAAA 0.624355 -108 GATTTGCGAATCATAAAAGAAAATAAAAAATA 6 210 0 TCATAAAAAA 0.898748 -83 ATCATAAGAATAATAAAAAGATAAGTATCATT 7 62 1 TAATAAAAAT 0.702414 -38 GTATCATTTTTGGGAAAAGTAAAA 7 86 1 TGGGAAAAAA 0.748629 -14 CTAACGCCCTTAATAAAACCAATTGAACCAGA 8 54 0 TAATAAAAAA 0.904684 -41 ******** ** Masking position 6 Map Score: 4.46394 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 654 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 6 TCAACCCCAAGCATTGGCTTTGTAAGCCTT 3 98 0 GCATTGGCTT 0.919341 -180 CCAATGCTTGGGGTTGAATTTTGCATAAAA 3 111 1 GGGTTGAATT 0.880505 -167 AGCCAATGTAGGGTGGGCTTAAGCCCACGC 4 117 1 GGGTGGGCTT 0.994903 -125 CTAGTTAAACGCGTGGGCTTAAGCCCACCC 4 127 0 GCGTGGGCTT 0.992594 -115 ACAGCCCGTAGGGTGGGAATAAACCCTAGT 4 152 0 GGGTGGGAAT 0.963415 -90 ********** Masking position 4 Map Score: 2.1878 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 44 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 GGGCGTAGTAAATACGCCCTTTGTAGTGAA 1 19 0 AATACGCCCT 0.971536 -36 GGGCGTATTTACTACGCCCTTTTCATTAAA 1 30 1 ACTACGCCCT 0.965867 -25 GTAGGGTGGGAATAAACCCTAGTTAAACGC 4 145 0 AATAAACCCT 0.84742 -97 GTGTCATCTAAATTTACCCTTTTGAAACAG 6 247 0 AATTTACCCT 0.933481 -46 GCGACTAAGCAATTTGCCCACCGCCTTTTT 7 19 0 AATTTGCCCA 0.944279 -81 TTTTACTTTTCCCAAAAATGATAC 7 86 0 ACTTTTCCCA 0.779548 -14 ********** Masking position 3 Map Score: 0.420907 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 97 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 TTTTTAATGAAAATTGATCTTTCGCGAAAG 2 69 0 AAATTGATCT 0.829664 -90 TAAAAAAATCCATCTTCAATACGAA 3 6 1 AAATCCATCT 0.968986 -272 AATAAACAAAAAATCCATCTTCGTATTGAA 3 25 0 AAATCCATCT 0.968986 -253 CCGAATTTTCAATTCCAGCTAATGTAGCCA 4 92 1 AATTCCAGCT 0.967032 -150 TACTTAAAAAAATTTCGGCTAGTATAGCAA 5 27 0 AATTTCGGCT 0.87222 -36 AGTATAACCGAATTTCATTT 5 53 1 AATTTCATTT 0.776297 -10 ********** Masking position 4 Map Score: 0.801362 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 182 Number in noncoding regions = 20 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: -1.16286e-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: -1.16286e-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: -1.16286e-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