AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_Glycolysis_+_PPS_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 HI0556 85 oxidoreductase, putative (devB) #2 HI0557 82 H. influenzae predicted coding region HI0557 #3 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #4 HI0559 194 sulfite synthesis pathway protein (cysQ) #5 HI0559.1 56 H. influenzae predicted coding region HI0559.1 #6 HI0561 300 conserved hypothetical protein #7 HI1302 147 asparaginyl-tRNA synthetase (asnS) #8 HI1573 300 pyruvate kinase, type II (pykA) #9 HI1574 33 replicative DNA helicase (dnaB) #10 HI1576 54 glucose-6-phosphate isomerase (pgi) Motif number 1 AGGTAAGCATTTGCAACAGTTTTATCAAAAACAGG 4 138 1 TTAATTTTAT 0.932969 -57 AATGAACTGTTATTAAAAATTTTATTCTTTAATAG 6 46 1 TAAATTTTAT 0.89495 -255 TTTTATTCTTTAATAGGATTTTTATTAAATGAAAA 6 65 1 TAGATTTTAT 0.93144 -236 AATGTTTAAATTAACCTGTTTTTATTTTTTTTTCA 6 94 0 TTCGTTTTAT 0.941185 -207 AACAGGTTAATTTAAACATTTTTCAATAAAACAAA 6 109 1 TTAATTTTCA 0.782263 -192 CATTTTTCAATAAAACAAATTTTATGTTAAAAAAA 6 125 1 TACATTTTAT 0.941864 -176 TTGTCAAAAATTTGACTATTTTTCAAGTTTTTTTA 6 152 0 TTCATTTTCA 0.872626 -149 GGTGCATTGATTACGGTAATTTTCACTGCATCCAA 6 275 1 TTGATTTTCA 0.851723 -26 TTAATAAGGCTTTACCCTATTTTATTTAGGACTCA 7 31 1 TTCTTTTTAT 0.754089 -117 GGACTCATTTTTAAGGCGATTTTATTGTTCATAAC 7 59 1 TTGGTTTTAT 0.930639 -89 TAAGGTAAACTATCGGCAATTTTAT 7 133 1 TAGATTTTAT 0.93144 -15 TAGTCGTGATTATAGATATTTTTAACTTGAACACA 8 94 1 TAAATTTTAA 0.839066 -207 TTTTGCCAGTTATATCGGGTTTTAAGAAAAATACT 8 129 0 TACGTTTTAA 0.857026 -172 GCTCAGTTATTTAAGCTGGTTTTGTTTACTTTTTT 8 160 0 TTCGTTTTGT 0.716233 -141 CGTTTTTGATTTCCAAAAGTTTTAAGCGTATAATG 8 195 1 TTAATTTTAA 0.894631 -106 TTTCTGGAATTTTTATTAGGGAGAAT 10 39 0 TTGATTTTAT 0.956893 -16 ** * * ****** Masking position 10 Map Score: 14.4239 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 391 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 GATTGGTTTTTTTCTCTAGAATACGGCATTATTTT 3 18 1 TTTTAAATAG 0.869302 -58 TTGCAACAGTTTTATCAAAAACAGGTTCATGTTGA 4 148 1 TTTAAAACAG 0.743384 -47 TGTTGTCTTCTTTCAATTCAACATGAACCTGTTTT 4 165 0 TTTTTAACAG 0.970148 -30 ATCCTTAAATTTATTTTAGAATAGGTTATCTTCTG 5 14 1 TTATAAATAG 0.641375 -43 TTTTGATTCGACAAAATAGTACCAC 6 1 1 TTTTTGACAA 0.813684 -300 ATTAAAAATTTTATTCTTTAATAGGATTTTTATTA 6 57 1 TTATTAATAG 0.776409 -244 TTTTATTTTTTTTTCATTTAATAAAAATCCTATTA 6 75 0 TTTTTAATAA 0.921659 -226 TTTAAACATTTTTCAATAAAACAAATTTTATGTTA 6 119 1 TTTTAAACAA 0.937837 -182 TAAAACAAATTTTATGTTAAAAAAACTTGAAAAAT 6 135 1 TTTTTAAAAA 0.747012 -166 TTCTTTTAAGTTTTCGTTATACATAAATTGTTCCT 6 216 0 TTTTTTACAA 0.746724 -85 TAAAGCCTTATTAATATTGAATATACGCGATTTT 7 10 0 TTATTAATAA 0.761958 -138 ATGAAGGAAATTTTCCATAAAAATATAGTGTTGGT 7 98 0 TTTATAAAAA 0.47328 -50 TATAGATATTTTTAACTTGAACACAAGTATTTTTC 8 104 1 TTTTTAACAA 0.96769 -197 ACACAAGTATTTTTCTTAAAACCCGATATAACTGG 8 124 1 TTTTAAACCG 0.694282 -177 CGCTCTTTTATTTTAACATATTTAGATTGT 9 14 0 TTTTTAACAA 0.967515 -20 *** ** **** * Masking position 11 Map Score: 11.0203 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 404 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 ACGATCATCACCCCACCAAAAATGCAGAT 1 67 0 ACCCCACCAA 0.978287 -19 GCGTGGCTAAAGCCCACCCTACATTAGATT 2 13 0 AGCCCACCCT 0.993948 -70 GGTGGGCTTTAGCCCACAATTTATTATGTT 2 50 0 AGCCCACAAT 0.946367 -33 TGTGGGCTAAAGCCCACCCTACGGAAAATC 2 62 1 AGCCCACCCT 0.993948 -21 AAAAGAAAACCGCGCAACCTTGTCAAAAAT 6 176 0 CGCGCAACCT 0.915668 -125 TTGTTCATAACCCGCACCAACACTATATTT 7 83 1 CCCGCACCAA 0.958261 -65 GAACCAGTGACCCCCACCATGTCAAGGTGG 8 26 1 CCCCCACCAT 0.992068 -275 ********** Masking position 6 Map Score: 8.78374 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 75 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 GTAAGAGCGTGGCTAAAGCCCACCCTACATT 2 18 0 GGTAAAGCCC 0.997094 -65 ATAAATTGTGGGCTAAAGCCCACCCTACGGA 2 56 1 GGTAAAGCCC 0.997094 -27 AAATAAAATAGGGTAAAGCCTTATTAATATT 7 27 0 GGTAAAGCCT 0.985076 -121 GGGGGTCACTGGTTCGAGTCCAGCTAGTCG 8 10 0 GGTCGAGTCC 0.969796 -291 TAGCTCAGTTGGTTAGAGCACCACCTTGACA 8 45 0 GGTAGAGCAC 0.986169 -256 ** ******** Masking position 7 Map Score: 4.92641 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 10 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 GGCTTTAGCCACGCTCTTACTAACATAATAAATTGTGG 2 29 1 ACGTTATCAA 0.972778 -54 TCTCTAGAATACGGCATTATTTTCGACATTACTCGGAA 3 30 1 ACGTTATCCA 0.904685 -46 ATTTGTAATGCCGTGGTTGCTGCCAAAAACAAGAGAAT 4 39 1 CCGTTGTCAA 0.988823 -156 AATCAATGCACCGAGGATAATTCCTCAAACGGTCAATT 6 249 0 CCGATATCAA 0.989836 -52 ATTGGATGCAGTGAAAATTACCGTAATCAATGCACC 6 275 0 CAGAAATCAA 0.799252 -26 TTCTTAAAACCCGATATAACTGGCAAAAAAGTAAACAA 8 136 1 CCGTAATCAA 0.982817 -165 AATAACTGAGCCGTTTTTGATTTCCAAAAGTTTTAAGC 8 184 1 CCGTTGTCAA 0.988823 -117 TATTTACTCCGTCAATAATTACAAAATTTTAAAGGT 8 275 0 CCGATATCAA 0.989836 -26 *** *** * * ** Masking position 18 Map Score: 5.57933 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 68 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 TTCGATTGGTTTTTTTCTCTAGAATACGGC 3 15 1 TTTTTTCTCT 0.972067 -61 GGAATGGTATTTTATGCTCTATTTGTAATG 4 19 1 TTTATGCTCT 0.899226 -176 TCAGCATAAAATTATTCTCTTGTTTTTGGC 4 60 0 ATTATTCTCT 0.905446 -135 TGGATAGCCTATTTTTCACT 5 47 1 ATTTTTCACT 0.905446 -10 TATTAAAAATTTTATTCTTTAATAGGATTT 6 56 1 TTTATTCTTT 0.856794 -245 GTTTTTATTTTTTTTTCATTTAATAAAAAT 6 82 0 TTTTTTCATT 0.856794 -219 GATTATAGATATTTTTAACTTGAACACAAG 8 101 1 ATTTTTAACT 0.758359 -200 AACTGAGCCGTTTTTGATTTCCAAAAGTTT 8 187 1 TTTTTGATTT 0.646289 -114 TGTGCACCGATTTTTTATCTGGCTAATATG 8 228 1 TTTTTTATCT 0.919391 -73 ********** Masking position 5 Map Score: 4.80103 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 354 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 7 AAAGCCCACCCTACGGAAAATCA 2 70 1 CTAGGAAAAT 0.856695 -13 GGAAGCCGAATAAGGAATAATT 3 64 1 TAAGAATAAT 0.80066 -12 ATGCTGACGCTAACGAACATTTACTTAACCA 4 83 1 TAAGAACATT 0.669712 -112 TAATGAACTGTTATTAAAAATTTTATTCTTT 6 45 1 TTATAAAAAT 0.810856 -256 TTTTTTTCATTTAATAAAAATCCTATTAAAG 6 72 0 TTATAAAAAT 0.810857 -229 AAATTTGTTTTATTGAAAAATGTTTAAATTA 6 116 0 TATGAAAAAT 0.721915 -185 TTTTTAAGCTCAAGGAACAATTTATGTATAA 6 204 1 CAAGAACAAT 0.846876 -97 AATTTATGTATAACGAAAACTTAAAAGAATT 6 222 1 TAAGAAAACT 0.808459 -79 TTGGTGCGGGTTATGAACAATAAAATCGCCT 7 72 0 TTAGAACAAT 0.956463 -76 CACTATATTTTTATGGAAAATTTCCTTCATT 7 103 1 TTAGGAAAAT 0.945203 -45 ATATCGGGTTTTAAGAAAAATACTTGTGTTC 8 122 0 TTAGAAAAAT 0.968608 -179 GGAATTTTTATTAGGGAGAATGACTCCCTCT 10 29 0 TTAGGAGAAT 0.820837 -26 *** ******* Masking position 7 Map Score: 6.7942 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 383 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 8 CTAGAGAAAAAAACCAATCGAACCAA 3 4 0 AAACAAGAAC 0.968653 -72 AACCACGGCATTACAAATAGAGCATAAAATACC 4 24 0 TTACAAGAGC 0.867322 -171 GTTGCTGCCAAAAACAAGAGAATAATTTTATGC 4 54 1 AAAAAAGAAT 0.701758 -141 CCTTGAGCTTAAAAAAAGAAAACCGCGCAACCT 6 186 0 AAAAAAAAAC 0.728279 -115 ACGAAAACTTAAAAGAATTGACCGTTTGAGGAA 6 234 1 AAAAAAGACC 0.933682 -67 GGTGGTGCTCTAACCAACTGAGCTATAGTCGCA 8 51 1 TAACAAGAGC 0.976453 -250 GCAAAAAAGTAAACAAAACCAGCTTAAATAACT 8 158 1 AAACAACAGC 0.928996 -143 AAAACCAGCTTAAATAACTGAGCCGTTTTTGAT 8 172 1 TAAAAAGAGC 0.969888 -129 TAAATATGTTAAAATAAAAGAGCG 9 20 1 AAAAAAGAGC 0.983975 -14 **** ** **** Masking position 7 Map Score: 4.65757 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 123 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 TACCGTAATCAATGCACCGAGGATAATTCC 6 263 0 AATGCACCGA 0.979021 -38 ATTGGATGCAGTGAAAATTACCGT 6 287 0 GATGCAGTGA 0.96206 -14 AAGCGTATAATGTGCACCGATTTTTTATCT 8 218 1 TGTGCACCGA 0.954587 -83 ATCTGGCTAATATGTAGCGAAGTAAAATAA 8 244 1 TATGTAGCGA 0.9287 -57 CTGTTCAAAAAATGCAGTGA 10 1 0 AATGCAGTGA 0.967917 -54 ********** Masking position 6 Map Score: 0.571608 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 65 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 ********** No masking Map Score: 3.24961e-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: 3.24961e-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 12 ********** No masking Map Score: 3.24961e-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