AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_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 CCAAATCACCTTATGCGGAACAAATTAACTGGAAAAATCTGCATTTT 1 31 1 TTAAATTAAA 0.853998 -55 TAATGCCGTATTCTAGAGAAAAAAACCAATCGAACCAA 3 2 0 TTAAAACAAA 0.926506 -74 TGTAATGCCGTGGTTGCTGCCAAAAACAAGAGAATAATTTTATGCTG 4 42 1 TTAAAAAAAA 0.971771 -153 AACATGAACCTGTTTTTGATAAAACTGTTGCAAATGCTTACCTGATT 4 134 0 TTAAACTAAC 0.875169 -61 ATCCAGAAGATAACCTATTCTAAAATAAATTTAAGGATTAA 5 5 0 TCAAAATAAA 0.907112 -52 ATAAAAATCCTATTAAAGAATAAAATTTTTAATAACAGTTCATTAGC 6 43 0 TTAAAATTAA 0.859532 -258 AATAGGATTTTTATTAAATGAAAAAAAAATAAAAACAGGTTAATTTA 6 76 1 TTAAAAAAAA 0.971771 -225 AACATAAAATTTGTTTTATTGAAAAATGTTTAAATTAACCTGTTTTT 6 106 0 TTAAAAAAAA 0.971771 -195 ATAAAACAAATTTTATGTTAAAAAAACTTGAAAAATAGTCAAATTTT 6 134 1 TTAAAAAAAA 0.971811 -167 ATTGGATGCAGTGAAAATTACCGTAATCAATGCACCGAG 6 272 0 TAAAAATAAA 0.920711 -29 CCTTAAAAATGAGTCCTAAATAAAATAGGGTAAAGCCTTATTAATAT 7 28 0 GTAAAATAAC 0.768512 -120 TTGGTGCGGGTTATGAACAATAAAATCGCCTTAAAAATGAGTCCTAA 7 56 0 TTAAAATAAA 0.984965 -92 ACCAACACTATATTTTTATGGAAAATTTCCTTCATTAAGGTAAACTA 7 98 1 TTAAAATCAA 0.898692 -50 AAAATACTTGTGTTCAAGTTAAAAATATCTATAATCACGACTACTTC 8 90 0 TTAAAATAAA 0.985232 -211 TAAAACCCGATATAACTGGCAAAAAAGTAAACAAAACCAGCTTAAAT 8 140 1 TAAAAAAAAC 0.7006 -161 TCGGTGCACATTATACGCTTAAAACTTTTGGAAATCAAAAACGGCTC 8 191 0 TTAAACTAAA 0.947085 -110 * * ***** ** * Masking position 14 Map Score: 15.8526 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 245 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 ATCTGCATTTTTGGTGGGGTGATGATCGT 1 67 1 TTGGTGGGGT 0.979608 -19 AATCTAATGTAGGGTGGGCTTTAGCCACGC 2 13 1 AGGGTGGGCT 0.994321 -70 AACATAATAAATTGTGGGCTAAAGCCCACC 2 50 1 ATTGTGGGCT 0.94953 -33 GATTTTCCGTAGGGTGGGCTTTAGCCCACA 2 62 0 AGGGTGGGCT 0.994321 -21 ATTTTTGACAAGGTTGCGCGGTTTTCTTTT 6 176 1 AGGTTGCGCG 0.92049 -125 AAATATAGTGTTGGTGCGGGTTATGAACAA 7 83 0 TTGGTGCGGG 0.960752 -65 CCACCTTGACATGGTGGGGGTCACTGGTTC 8 26 0 ATGGTGGGGG 0.992557 -275 ********** Masking position 5 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 3 GTTATTATTTAAAACCCTAGCC 1 3 1 TATTATTTAA 0.825413 -83 GCCCACAATTTATTATGTTAGTAAGAGCGT 2 39 0 TATTATGTTA 0.580928 -44 TTTGCAACAGTTTTATCAAAAACAGGTTCA 4 147 1 TTTTATCAAA 0.475083 -48 TAATCCTTAAATTTATTTTAGAATAGGTTA 5 12 1 ATTTATTTTA 0.667505 -45 GCTAATGAACTGTTATTAAAAATTTTATTC 6 43 1 TGTTATTAAA 0.739089 -258 TTAAAAATTTTATTCTTTAATAGGATTTTT 6 58 1 TATTCTTTAA 0.616498 -243 TTAATAGGATTTTTATTAAATGAAAAAAAA 6 74 1 TTTTATTAAA 0.868031 -227 ATTAACCTGTTTTTATTTTTTTTTCATTTA 6 90 0 TTTTATTTTT 0.766283 -211 ATAAAATTTGTTTTATTGAAAAATGTTTAA 6 120 0 TTTTATTGAA 0.889988 -181 ATAAAACAAATTTTATGTTAAAAAAACTTG 6 134 1 TTTTATGTTA 0.837535 -167 GGTTGCGCGGTTTTCTTTTTTTAAGCTCAA 6 187 1 TTTTCTTTTT 0.527101 -114 CTTTACCCTATTTTATTTAGGACTCATTTT 7 40 1 TTTTATTTAG 0.704674 -108 TTTAAGGCGATTTTATTGTTCATAACCCGC 7 68 1 TTTTATTGTT 0.601406 -80 AACACTATATTTTTATGGAAAATTTCCTTC 7 101 1 TTTTATGGAA 0.746388 -47 ACACAAGTATTTTTCTTAAAACCCGATATA 8 124 1 TTTTCTTAAA 0.694934 -177 AAAACGGCTCAGTTATTTAAGCTGGTTTTG 8 171 0 AGTTATTTAA 0.512932 -130 ATTTTAAAGGTGTTATTTTACTTCGCTACA 8 256 0 TGTTATTTTA 0.857003 -45 CGCTCTTTTATTTTAACATATTTAG 9 19 0 TTTTATTTTA 0.93409 -15 ********** Masking position 6 Map Score: 10.2427 Number of sites scoring better than the average of aligned sites = 1119 Number in coding regions = 719 Number in noncoding regions = 400 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 4 ATTAACTGGAAAAATCTGCATTTTTGGTGGGGTGA 1 54 1 AATCGCTTTT 0.914292 -32 GTAATGTCGAAAATAATGCCGTATTCTAGAGAAAA 3 27 0 ATAAGCTATT 0.577949 -49 GCGGAATGGTATTTTATGCTCTATTTGTAATGCCG 4 17 1 ATTAGCTATT 0.846601 -178 TCAGGTAAGCATTTGCAACAGTTTTATCAAAAACA 4 136 1 ATGCACTTTT 0.633581 -59 TTTCAATTCAACATGAACCTGTTTTTGATAAAACT 4 155 0 ATGACCTTTT 0.958933 -40 GGCTATCCAGAAGATAACCTATTCTAAAATAAATT 5 21 0 AATACCTTCT 0.686411 -36 GGTTATCTTCTGGATAGCCTATTTTTCACT 5 37 1 TATACCTTTT 0.753727 -20 AAAAATGTTTAAATTAACCTGTTTTTATTTTTTTT 6 97 0 ATTACCTTTT 0.96938 -204 ATTTTTGACAAGGTTGCGCGGTTTTCTTTTTTTAA 6 176 1 ATTGGCTTTT 0.856917 -125 ATTAATATTGAATATACGCGATTTT 7 1 0 AATAGCTTTT 0.921269 -147 TATTAATAAGGCTTTACCCTATTTTATTTAGGACT 7 29 1 GTTACCTTTT 0.833774 -119 TAGGACTCATTTTTAAGGCGATTTTATTGTTCATA 7 57 1 TTAAGCTTTT 0.59688 -91 ATTAAGGTAAACTATCGGCAATTTTAT 7 131 1 AATCGCTTTT 0.913998 -17 CAGCTTAAATAACTGAGCCGTTTTTGATTTCCAAA 8 177 1 ATGACCTTTT 0.95772 -124 TAAGCGTATAATGTGCACCGATTTTTTATCTGGCT 8 217 1 ATGCCCTTTT 0.939335 -84 * *** ** **** Masking position 12 Map Score: 10.3329 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 424 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 GTAAGAGCGTGGCTAAAGCCCACCCTACATT 2 18 0 GGTAAAGCCC 0.996864 -65 ATAAATTGTGGGCTAAAGCCCACCCTACGGA 2 56 1 GGTAAAGCCC 0.996864 -27 AAATAAAATAGGGTAAAGCCTTATTAATATT 7 27 0 GGTAAAGCCT 0.983901 -121 GGGGGTCACTGGTTCGAGTCCAGCTAGTCG 8 10 0 GGTCGAGTCC 0.967455 -291 TAGCTCAGTTGGTTAGAGCACCACCTTGACA 8 45 0 GGTAGAGCAC 0.985077 -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 6 AAATGCAGATTTTTCCAGTTAATTTGTTCC 1 47 0 TTTTCCAGTT 0.969749 -39 TTTTTATTTTTTTTTCATTTAATAAAAATC 6 81 0 TTTTTCATTT 0.69296 -220 ATTTGACTATTTTTCAAGTTTTTTTAACAT 6 148 0 TTTTCAAGTT 0.970331 -153 CGGTTTTCTTTTTTTAAGCTCAAGGAACAA 6 194 1 TTTTTAAGCT 0.921111 -107 ACGGTCAATTCTTTTAAGTTTTCGTTATAC 6 229 0 CTTTTAAGTT 0.845598 -72 AAAATACTTGTGTTCAAGTTAAAAATATCT 8 107 0 TGTTCAAGTT 0.909612 -194 TGTTTACTTTTTTGCCAGTTATATCGGGTT 8 143 0 TTTGCCAGTT 0.894898 -158 ACGGCTCAGTTATTTAAGCTGGTTTTGTTT 8 168 0 TATTTAAGCT 0.707941 -133 ********** Masking position 7 Map Score: 2.39907 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 238 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 GGAATTATCCTCGGTGCATTGATTACGGTA 6 263 1 TCGGTGCATT 0.981599 -38 ACGGTAATTTTCACTGCATCCAAT 6 287 1 TCACTGCATC 0.966652 -14 AGATAAAAAATCGGTGCACATTATACGCTT 8 218 0 TCGGTGCACA 0.960045 -83 TTATTTTACTTCGCTACATATTAGCCAGAT 8 244 0 TCGCTACATA 0.937065 -57 TCACTGCATTTTTTGAACAG 10 1 1 TCACTGCATT 0.971821 -54 ********** Masking position 5 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 8 ********** 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 9 ********** 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 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