AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_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 HI0478 29 ATP synthase F1, subunit epsilon (atpC) #2 HI0483 49 ATP synthase F0, subunit b (atpF) #3 HI0484 55 ATP synthase F0, subunit c (atpE) #4 HI0485 36 ATP synthase F0, subunit a (atpB) #5 HI0485.1 125 H. influenzae predicted coding region HI0485.1 #6 HI0486 139 glucose-inhibited division protein (gidB) #7 HI0487 115 H. influenzae predicted coding region HI0487 Motif number 1 AATCGATCCTTTGTTCTGAAGAAGAATAACCCAA 4 13 0 TTGTTAAGAG 0.947123 -24 ATAGATAAATTATTTTCTAAAAGTGTGATTTATAT 5 21 1 TTTTTAAATG 0.992786 -105 ACACTTTTTATGTGTTTTTAAGTTGAATCTAAAGC 5 57 1 TTGTTAAGTG 0.982664 -69 GGGCTAAAATTATTTTGTAAAAGTG 5 111 1 TTTTTAAATG 0.992786 -15 GCATTCAATTTATGGTGTAAAACTGGACATTGATT 6 24 1 TTGTTAAATG 0.99145 -116 AATTACGCTATTTTACTTAAAAGTGCGGTAAATTT 6 96 0 TTTCTAAATG 0.985657 -44 TAAAATAGCGTAATTTTTCAAAGAGATAATAAAT 6 116 1 TATTTAAAAG 0.874924 -24 TAGATCACAGTTTTGTAGCAAAATGGTAAAAAAAT 7 27 0 TTTTGAAATG 0.985615 -89 TGCACTGTTTTATTTCAGTAAAGTGCGGTAAATTA 7 62 1 TTTCGAAATG 0.971086 -54 * ** * * *** ** Masking position 10 Map Score: 13.414 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 98 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 GCCCTAGAGCCGGTTAATAAAAAACGA 3 8 0 CGGTTAATAA 0.984525 -48 GACATTGATTCGGTAAATAATTCATCAAAT 6 49 1 CGGTAAATAA 0.995247 -91 CTTAAAAGTGCGGTAAATTTCCTTAATGTT 6 86 0 CGGTAAATTT 0.977984 -54 TGTAGCAAAATGGTAAAAAAATTTGTAAGG 7 19 0 TGGTAAAAAA 0.92422 -97 CAGTAAAGTGCGGTAAATTAGCGAACAAAT 7 77 1 CGGTAAATTA 0.993204 -39 ********** Masking position 6 Map Score: 7.11303 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 118 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 ACAAATAGATAAATTATTTTCTAAAAGTGTGAT 5 17 1 AAATTTTTTA 0.967538 -109 TTATTTTCTAAAAGTGTGATTTATATAACACTT 5 30 1 AAAGTTGTTA 0.969524 -96 CGGCGGGCTAAAATTATTTTGTAAAAGTG 5 107 1 AAATTTTTTA 0.967538 -19 AGGTGCATTCAATTTATGGTGTAAAACTGGACA 6 20 1 AATTTTGTTA 0.96718 -120 AAATTTCCTTAATGTTTTTAGTAATTTGATGAA 6 69 0 AATGTTTATA 0.886277 -71 CATCCTTACAAATTTTTTTACCATTTTGCTACA 7 16 1 AATTTTTACA 0.754668 -100 TTTTGCTACAAAACTGTGATCTATGCACTGTTT 7 39 1 AAACTTGTTA 0.945314 -77 ATTAGCGAACAAATTTTGAACTAACAAAAACAA 7 93 1 AAATTTGATA 0.967177 -23 ***** ** * ** Masking position 2 Map Score: 5.80688 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 167 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 4 TTTGTTCTCCTTCAAATGACTT 1 18 0 TGTTCTCCTT 0.958325 -12 TTACTATGCTTGTTTTACGTTGATAAGCAA 2 20 0 TGTTTTACGT 0.975126 -30 CTTTGGGTTATTCTTCTTCAGAACAAAG 4 9 1 TATTCTTCTT 0.914488 -28 ATTTCCTTAATGTTTTTAGTAATTTGATGA 6 70 0 TGTTTTTAGT 0.882521 -70 AAAATTACGCTATTTTACTTAAAAGTGCGG 6 103 0 TATTTTACTT 0.940802 -37 ATCTATGCACTGTTTTATTTCAGTAAAGTG 7 57 1 TGTTTTATTT 0.917788 -59 TTGTTTTTGTTAGTTCAAAAT 7 105 0 TGTTTTTGTT 0.943006 -11 ********** Masking position 6 Map Score: 4.36542 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 320 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 5 GTGTTATATAAATCACACTTTTAGAAAATA 5 31 0 AATCACACTT 0.939467 -95 GTGTGATTTATATAACACTTTTTATGTGTT 5 43 1 TATAACACTT 0.911286 -83 TAAGGAAATTTACCGCACTTTTAAGTAAAA 6 91 1 TACCGCACTT 0.994471 -49 TTAAGTAAAATAGCGTAATTTTTCAAAGAG 6 111 1 TAGCGTAATT 0.786831 -29 TTCGCTAATTTACCGCACTTTACTGAAATA 7 72 0 TACCGCACTT 0.994471 -44 ********** Masking position 7 Map Score: 1.84609 Number of sites scoring better than the average of aligned sites = 1690 Number in coding regions = 1165 Number in noncoding regions = 525 Number of orfs with sites within 600 bp upstream = 334 Fraction of orfs with sites within 600 bp upstream = 0.053646 Motif number 6 TCACCTTATTTGCTTATCAACGTAA 2 6 1 TTATTTGCTT 0.88777 -44 CCAATAGAAGTTAAGTTTTAGCCCTAGAGC 3 28 0 TTAAGTTTTA 0.848548 -28 AATAATTTATCTATTTGTTACTTT 5 5 0 CTATTTGTTA 0.802589 -121 AATAGATAAATTATTTTCTAAAAGTGTGAT 5 20 1 TTATTTTCTA 0.928298 -106 ATAACACTTTTTATGTGTTTTTAAGTTGAA 5 54 1 TTATGTGTTT 0.903404 -72 CGGGCTAAAATTATTTTGTAAAAGTG 5 110 1 TTATTTTGTA 0.928298 -16 TGCATTCAATTTATGGTGTAAAACTGGACA 6 23 1 TTATGGTGTA 0.877839 -117 GTAAATTTCCTTAATGTTTTTAGTAATTTG 6 74 0 TTAATGTTTT 0.668653 -66 ********** Masking position 3 Map Score: 1.32396 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 519 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 7 ********** No masking Map Score: -3.6705e-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: -3.6705e-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: -3.6705e-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