AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_hinf_reg_100.orf -o00190_hinf_100.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 HI0124 234 inorganic pyrophosphatase (ppa) #2 HI0478 29 ATP synthase F1, subunit epsilon (atpC) #3 HI0483 49 ATP synthase F0, subunit b (atpF) #4 HI0484 55 ATP synthase F0, subunit c (atpE) #5 HI0485 36 ATP synthase F0, subunit a (atpB) #6 HI0485.1 125 H. influenzae predicted coding region HI0485.1 #7 HI0835 181 fumarate reductase, flavoprotein subunit (frdA) Motif number 1 ACTTCCAATTTTTTACTTAACTTCAAGGAACACT 1 10 0 TTTTCTATTA 0.778253 -225 AGGTGCGCTATTTTACATCATAAAAACGATAAGTA 1 49 1 TTTTCTAAAA 0.976377 -186 TTGACCGCACTTTATCCTAAATAAAACTCACGCAA 1 89 0 TTTACTATAA 0.848715 -146 TGTTGCGTTTTTTAACTTGATAAAATGAAGGAAAC 1 207 1 TTTACTAAAA 0.95626 -28 TTTGTTCTCCTTCAAATGACTTGAAGTGA 2 11 0 TTCTCTAATA 0.949956 -19 AATTTTCTCCAATAGAAGTTAAGTTTTAG 4 37 0 TTCTCAAAAT 0.883189 -19 CTTTGGGTTATTCTTCTTCAGAACAAAGGATCGAT 5 11 1 TTCTCTAAAA 0.987092 -26 TGGCTTTAGATTCAACTTAAAAACACATAAAAAGT 6 59 0 TTCACTAAAA 0.968225 -67 CACTTTTACAAAATAATTTTAGCCCGCC 6 108 0 TTTTCAAAAT 0.849188 -18 GGATTTTGTGATCTACCTCAAAAAAGCTAAGATTG 7 35 0 ATCTCTAAAA 0.906645 -147 CATTGTGCCATTTTTCGTTACAAATTAATAACGT 7 97 0 TTTTCTAAAT 0.95702 -85 **** * * * ** * Masking position 10 Map Score: 13.1722 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 277 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 GCACCTTATTACTTCCAATTTTTTACTTAACTTCAA 1 19 0 ATTCTTTTTC 0.963656 -216 GCAAACGTTTACTTATCGTTTTTATGATGTAAAATA 1 57 0 ATTTTTTTTG 0.762428 -178 ATCTCATAACTATTCATAATTTTGACCGCACTTTAT 1 109 0 TTTAATTTTC 0.613597 -126 AGATGGATCTATTTGCTGATTTTCTCTACAAATGAG 1 141 1 ATTCATTTTC 0.904095 -94 ACGCAACAAGTATAGCAGTTTTCTGCGAACTCGCA 1 179 0 TTACTTTTG 0.948162 -56 CTGCTATACTTGTTGCGTTTTTTAACTTGATAAAAT 1 197 1 TTTCTTTTTC 0.980815 -38 TAGAAAATAATTTATCTATTTGTTACTTT 6 4 0 TTACTTTGTC 0.864409 -122 GTGTGATTTATATAACACTTTTTATGTGTTTTTAAG 6 43 1 TTACTTTTTG 0.980929 -83 CTCAACTCAATCTTAGCTTTTTTGAGGTAGATCACA 7 28 1 TTTGTTTTTG 0.90168 -154 AAGATGGAAAGTATCGGATTTTGTGATCTACCTCA 7 50 0 TACATTTTG 0.90464 -132 GTTACAAATTAATAACGTTTTTATGTCTAAAGATG 7 80 0 ATACTTTTG 0.904639 -102 GCCCACACAATATTACCCTTTTAGGGGATTTATTTT 7 131 1 TTTCTTTTAG 0.891343 -51 * ** * ***** * Masking position 10 Map Score: 12.8157 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 538 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 3 ATAAGGTGCGCTATTTTACATCATAAAAAC 1 46 1 CTATTTTACA 0.916318 -189 AAAAACGCAACAAGTATAGCAGTTTTCTG 1 189 0 CAAGTATAGC 0.879929 -46 ATATAAATCACACTTTTAGAAAATAATTTA 6 26 0 CACTTTTAGA 0.952195 -100 TTTAGCCCGCCGATTATACCTTTGCTGGCT 6 89 0 CGATTATACC 0.851061 -37 TTTTACAAAATAATTTTAGCCCGCCGATTA 6 103 0 TAATTTTAGC 0.823044 -23 CACTTTTACAAAATAATTTT 6 116 0 CACTTTTACA 0.961047 -10 GAGAGTAGCTCTCGTTTACA 7 1 0 CTCGTTTACA 0.815324 -181 ACTCTCAACTCAATCTTAGCTTTTTTGAGG 7 25 1 CAATCTTAGC 0.926478 -157 AATGCCCACACAATATTACCCTTTTAGGGG 7 128 1 CAATATTACC 0.91328 -54 ********** Masking position 7 Map Score: 3.34675 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 586 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 TTTGTTTCCTTCATTTTATCAAGT 1 221 0 TTTCCTTCAT 0.953915 -14 TTTGTTCTCCTTCAAATGACTT 2 18 0 TGTTCTCCTT 0.966773 -12 AACGTCCTCCTTACTATGCTTG 3 38 0 CGTCCTCCTT 0.948693 -12 AATTTTCTCCAATAGAAGTTAA 4 44 0 TTTTCTCCAA 0.900047 -12 CTTTGGGTTATTCTTCTTCAGAACAAAG 5 9 1 TATTCTTCTT 0.901062 -28 ATCCGATACNTTTCCATCTTTAGACATAAA 7 66 1 TTTCCATCTT 0.848383 -116 GATATCCTCCAATCAATAGAAA 7 170 0 TATCCTCCAA 0.928465 -12 ********** Masking position 3 Map Score: 2.44161 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 102 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 TAAAATAGCGCACCTTATTACTTCCAATTT 1 34 0 CACCTTATTA 0.990436 -201 TCACCTTATTTGCTTATCAAC 3 2 1 CACCTTATTT 0.969209 -48 AACGTCCTCCTTACTATGCTTGTTTT 3 34 0 CTCCTTACTA 0.934124 -16 AGACATAAAANACGTTATTAATTTGTAACG 7 87 1 NACGTTATTA 0.880995 -95 ACAATGCCCACACAATATTACCCTTTTAGG 7 126 1 CACAATATTA 0.887926 -56 ********** Masking position 6 Map Score: 0.670071 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 54 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TTATGATGTAAAATAGCGCACCTTATTACTT 1 41 0 AATAGCGCAC 0.966631 -194 TTTATCCTAAATAAAACTCACGCAAACGTTT 1 83 0 AAAAACTCAC 0.921917 -152 GAAAATCAGCAAATAGATCCATCTCATAACT 1 134 0 AATAGATCCA 0.920334 -101 TTATCAAGTTAAAAAACGCAACAAGTATAGC 1 199 0 AAAAACGCAA 0.723256 -36 AAAGTAACAAATAGATAAATTATTTTCTA 6 9 1 AATAGATAAA 0.69495 -117 AAAAAGTGTTATATAAATCACACTTTTAGAA 6 35 0 AATAAATCAC 0.970505 -91 AGCTTTTTTGAGGTAGATCACAAAATCCGAT 7 42 1 AGTAGATCAC 0.932715 -140 TAGAAAGTAAAAATAAATCCCCTAAAAGGGT 7 145 0 AATAAATCCC 0.949064 -37 * ********* Masking position 5 Map Score: 1.9754 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 187 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 ********** No masking Map Score: 8.47978e-13 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 8 ********** No masking Map Score: 8.47978e-13 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: 8.47978e-13 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