AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00480_hinf_reg_300.orf -o00480_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 HI0111 300 glutathione transferase (bphH) #2 HI0161 215 glutathione reductase (gor) #3 HI0162 93 lipoprotein, putative #4 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #5 HI0559 194 sulfite synthesis pathway protein (cysQ) #6 HI0559.1 56 H. influenzae predicted coding region HI0559.1 #7 HI0561 300 conserved hypothetical protein Motif number 1 TGTAAGGCTTTGATAATAAAAAAGCGTGGAAAT 1 3 0 TTAAAAATAA 0.976361 -298 CTAATTGGCTTGAATACCAAAAAATTTAAAACAGTTATTGT 1 41 0 TAAAAAATAA 0.982717 -260 TCCAGAACATTACTCTAAAAAACATATCAAAGTATCTAAAT 1 148 1 TTAAAACTAA 0.971411 -153 AGTTAGATATTCCACGTATAAAACAGTATAATTCCATCAAT 1 244 1 TATAAAATAA 0.868177 -57 CATACTAGGCTTCACATAAAATCATTTCAAACTAATCATCT 2 76 1 TAAAATCTAA 0.844188 -140 TTCTGCCTAATTTTTATAAAGAATGCTATAAATTGATGTAA 2 150 0 TTAAGAATAA 0.876398 -66 ACAAAAAAATTTTAGTTTAAAAAAGGTTCAAACT 2 192 1 TAAAAAATAA 0.982717 -24 TGCCGTATTCTAGAGAAAAAAACCAATCGAACCAA 4 5 0 TAAAAACTAA 0.979069 -71 CATGAACCTGTTTTTGATAAAACTGTTGCAAATGCTTACCT 5 138 0 TTAAAACTAA 0.971411 -57 AGGATTTTTATTAAATGAAAAAAAAATAAAAACAGGTTAAT 7 79 1 TAAAAAATAA 0.982703 -222 ATAAAATTTGTTTTATTGAAAAATGTTTAAATTAACCTGTT 7 109 0 TTAAAAATAA 0.976342 -192 TAAAACAAATTTTATGTTAAAAAAACTTGAAAAATAGTCAA 7 135 1 TAAAAAATAA 0.982717 -166 * * ***** * ** Masking position 10 Map Score: 18.0815 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 154 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 2 TTTCCACGCTTTTTTATTATCAAAGCCTTA 1 12 1 TTTTTATTAT 0.743479 -289 CCAATTAGGAACTTTATTCTATTATAAAAT 1 74 1 ACTTTATTCT 0.891015 -227 CTATCACGCTATTTCATTCTACATACTAGG 2 55 1 ATTTCATTCT 0.883196 -161 TTATGAATATTTTTTACTCTTTTGAACAGA 2 114 0 TTTTTACTCT 0.847736 -102 CTAAAATTTTTTTGTATTCTGCCTAATTTT 2 177 0 TTTGTATTCT 0.81177 -39 ATACAAAAAAATTTTAGTTTAAAAAAGGTT 2 190 1 ATTTTAGTTT 0.877129 -26 ATAGCGTTTCATTTTAGTTTTTGTGGAGAA 3 17 0 ATTTTAGTTT 0.877129 -77 GCGGAATGGTATTTTATGCTCTATTTGTAA 5 17 1 ATTTTATGCT 0.971728 -178 CAAGAGAATAATTTTATGCTGACGCTAACG 5 68 1 ATTTTATGCT 0.971728 -127 TTAATCCTTAAATTTATTTTAGAATAGGTT 6 11 1 AATTTATTTT 0.686713 -46 GTTATTAAAAATTTTATTCTTTAATAGGAT 7 54 1 ATTTTATTCT 0.981073 -247 AATTAACCTGTTTTTATTTTTTTTTCATTT 7 91 0 TTTTTATTTT 0.921557 -210 AATAAAACAAATTTTATGTTAAAAAAACTT 7 133 1 ATTTTATGTT 0.931777 -168 CGGTTTTCTTTTTTTAAGCTCAAGGAACAA 7 194 1 TTTTTAAGCT 0.713535 -107 ********** Masking position 6 Map Score: 13.2049 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 212 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 TTTACGATTAAACAATAGTAAGAAGCAATTTTAATAA 1 208 1 AAAAAGAAGA 0.663673 -93 TAGCTCATAAACCAACAGGAGTATTTT 1 284 1 ACAAAGATTT 0.943894 -17 AGCGTGATAGAAAAAGAGGAAGATTGTTCAATCTTCC 2 28 0 AAAAAGATTT 0.986296 -188 GGAAGTTTGTAAGAATAGCACAATTCTAATTGATTTA 3 57 1 AAAAAGATTT 0.986307 -37 TGCTGCCAAAAACAAGAGAATAATTTTATGCTGACGC 5 56 1 AAAAAGATTT 0.985667 -139 CAGTTTTATCAAAAACAGGTTCATGTTGAATTGAAAG 5 154 1 AAAAAGATGT 0.958061 -41 ATGAACTGTTATTAAAAATTTTATTCTTTAATAGGAT 7 47 1 ATAAAAATTT 0.662483 -254 TTTTTCATTTAATAAAAATCCTATTAAAGAATAAAAT 7 64 0 AAAAAAATTA 0.849356 -237 AAAAAAAAATAAAAACAGGTTAATTTAAACATTTTTC 7 96 1 AAAAAGATTA 0.969923 -205 AAAAAACTTGAAAAATAGTCAAATTTTTGACAAGGTT 7 154 1 AAAAAGATTT 0.984383 -147 ** ** ** *** * Masking position 7 Map Score: 9.99381 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 64 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 TTACAATAACTGTTTTAAATTTTTTGGTATT 1 39 1 TGTTTAAATT 0.804204 -262 ACTTTATTCTATTATAAAATTATATCTATAA 1 84 1 ATATAAAATT 0.800252 -217 TAGAAAATTTATCTTTCAATTGACATCAATA 1 117 1 ATTTTCAATT 0.863889 -184 TGAACTAATATTATAACAATTTAGATACTTT 1 176 0 TTTAACAATT 0.768988 -125 AATATCTAACTTATTAAAATTGCTTCTTACT 1 224 0 TTTTAAAATT 0.856728 -77 ATAAAACCAATTACATCAATTTATAGCATTC 2 140 1 TTCATCAATT 0.779684 -76 ATAGCATTCTTTATAAAAATTAGGCAGAATA 2 162 1 TTTAAAAATT 0.802095 -54 AATTTCCCCATAAATCAATTAGAATTGTGC 3 74 0 ATAATCAATT 0.717224 -20 CGTTAGCGTCAGCATAAAATTATTCTCTTGT 5 67 0 AGATAAAATT 0.707828 -128 GCGTGTTGTCTTCTTTCAATTCAACATGAAC 5 172 0 TTTTTCAATT 0.8481 -23 TTAATCCTTAAATTTATTTTAGAA 6 4 1 ATCTTAAATT 0.878448 -53 ATCCTATTAAAGAATAAAATTTTTAATAACA 7 53 0 AGATAAAATT 0.707828 -248 TTATTGAAAAATGTTTAAATTAACCTGTTTT 7 107 0 ATTTTAAATT 0.885356 -194 CGCGCAACCTTGTCAAAAATTTGACTATTTT 7 165 0 TGCAAAAATT 0.696144 -136 AGTTTTCGTTATACATAAATTGTTCCTTGAG 7 212 0 ATCATAAATT 0.830458 -89 ** ******** Masking position 8 Map Score: 8.6304 Number of sites scoring better than the average of aligned sites = 847 Number in coding regions = 642 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 5 TTCAAGCCAATTAGGAACTTTATTCTATTAT 1 68 1 TTAGGAATTT 0.900895 -233 ATATCTACAGTGAGGAAGATTGAACAATCTT 2 15 1 TGAGGAAATT 0.972889 -201 TGATAGAAAAAGAGGAAGATTGTTCAATCTT 2 30 0 AGAGGAAATT 0.834696 -186 GTAATTGGTTTTATGAATATTTTTTACTCTT 2 123 0 TTATGAAATT 0.691104 -93 TTTATAAAAATTAGGCAGAATACAAAAAAAT 2 171 1 TTAGGCAAAT 0.745909 -45 TATACATTAATAAGGAAGTTTGTAAGAATAG 3 44 1 TAAGGAATTT 0.935827 -50 GGAAGCCGAATAAGGAATAATT 4 64 1 TAAGGAAAAT 0.961549 -12 ATGCTGACGCTAACGAACATTTACTTAACCA 5 83 1 TAACGAAATT 0.907321 -112 TTTTTAAGCTCAAGGAACAATTTATGTATAA 7 204 1 CAAGGAAAAT 0.839104 -97 AATTTATGTATAACGAAAACTTAAAAGAATT 7 222 1 TAACGAAACT 0.750769 -79 ATTGACCGTTTGAGGAATTATCCTCGGTGCA 7 250 1 TGAGGAATAT 0.907092 -51 ******* *** Masking position 7 Map Score: 6.14693 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 138 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 AAATTTTCTATGTTATAGATATAATTTTATA 1 96 0 TTTATAGATA 0.92697 -205 TTTAGAGTAATGTTCTGGATATTGATGTCAA 1 136 0 TTTCTGGATA 0.974901 -165 ATGTAATTGGTTTTATGAATATTTTTTACTC 2 125 0 TTTATGAATA 0.875969 -91 TCTGCCTAATTTTTATAAAGAATGCTATAAA 2 159 0 TTTATAAAGA 0.806937 -57 TCATTTTAGTTTTTGTGGAGAACTTATA 3 8 0 TTTGTGGAGA 0.948841 -86 AATAATGCCGTATTCTAGAGAAAAAAACCAA 4 20 0 TTTCTAGAGA 0.959011 -56 GAATAGGTTATCTTCTGGATAGCCTATTTTT 6 32 1 TTTCTGGATA 0.953596 -25 * ********* Masking position 9 Map Score: 4.08216 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 71 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AACAGTTATTGTAAGGCTTTGATAATAAAAA 1 22 0 GTAAGGTTTG 0.933124 -279 GTTTTTTAGAGTAATGTTCTGGATATTGATG 1 140 0 GTAATGTCTG 0.97755 -161 TCATTTCAAACTAATCATCTGTTCAAAAGAG 2 97 1 CTAATCTCTG 0.957762 -119 GTAAATGTTCGTTAGCGTCAGCATAAAATTA 5 76 0 GTTAGCTCAG 0.861856 -119 TACCAATCAGGTAAGCATTTGCAACAGTTTT 5 130 1 GTAAGCTTTG 0.948508 -65 TTTAGAATAGGTTATCTTCTGGATAGCCTAT 6 28 1 GTTATCTCTG 0.961371 -29 ACAAAGTATGCTAATGAACTGTTATTAAAAA 7 34 1 CTAATGACTG 0.79223 -267 ****** **** Masking position 4 Map Score: 1.45219 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 54 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ********** No masking Map Score: 2.09143e-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: 2.09143e-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: 2.09143e-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