AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i338_weak1_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 HI1556 59 2-hydroxyacid dehydrogenase #2 HI1560 22 H. influenzae predicted coding region HI1560 #3 HI1561 106 peptide chain release factor 1 (prfA) #4 HI1562 252 H. influenzae predicted coding region HI1562 #5 HI1563 32 conserved hypothetical protein #6 HI1564 32 H. influenzae predicted coding region HI1564 #7 HI1564.1 284 H. influenzae predicted coding region HI1564.1 Motif number 1 ATTTCATCAAAAGTGCGGTTAATTTTGACCGCAC 1 6 1 AAAAATGATT 0.97009 -54 CGCACTTTGTATATAAAAAAGGAGCAATTA 1 40 1 ATAAAAGATT 0.960831 -20 TAAGTCACCGAAAATAAAATCGGCGTATTCTAGCCGATT 3 75 0 AATAAAGATT 0.920581 -32 GGGCTTAAGACTGAAAAAAGTGAGCAATTTTGATCACTT 4 18 0 CAAAAAGATT 0.966468 -235 GGTGTGAAATGATTAAAAATTGAACTATTTAATTAGGAG 4 66 0 GTAAAAGATT 0.88571 -187 CTTTACAGAGAGTACAACAAAGCATAATTGGCAACTAGG 4 128 1 AACAAAGATT 0.983649 -125 TCAAAAACACACTAAAACAAGGCGACAATATGCTTGCTA 4 169 0 AAAAAAGAAT 0.960829 -84 CCTGATCTTCAAGAAAAAATTGAAGCAATTAAAGAAGAA 4 221 1 AAAAAAGAAT 0.96083 -32 GGTATCGACTCCTAAAAAACCGCAAGATTATA 5 4 0 CAAAAAGATT 0.966468 -29 AGCACGTTTAATCTAAAATTGGTCATATTTAGTCCTATA 7 43 1 ATAAATGATT 0.897065 -242 TTAGTCCTATAAAAAAAATAATAATAATTCTCAAACATA 7 71 1 AAAAATTATT 0.776857 -214 GTATTTTCTCACAACAATAAAGATTGATTTTTGATAAAA 7 124 1 AACAAAGATT 0.983738 -161 AAAATCAAGAAATAAAAACTATTCTTATTATTTTCTGTA 7 160 1 AAAAACTATT 0.793889 -125 CGCATTATAGGAAACAAGCAGGTTTAAATACAGAAAATA 7 188 0 GACAACGAAT 0.741729 -97 AGCCCACCAAAAAACAATCGAGAGATATT 7 266 1 AACAACGATT 0.971279 -19 * **** * * *** Masking position 7 Map Score: 19.788 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 428 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 2 CGCACTTTGTATATAAAAAAGGAGCAATTA 1 40 1 ATATAAAAAA 0.686097 -20 TGGGTAAATCACAAATAAAGCGTCT 3 6 1 AAATCACAAA 0.865658 -101 AGCGAAAAGGAAATTAAGAATCTCAGACGC 3 30 0 AAATTAAGAA 0.899982 -77 CTGTTTTGGCAAATCAAAAACACACTAAAA 4 191 0 AAATCAAAAA 0.943786 -62 TTGAAGCAATTAAAGAAGAATTG 4 240 1 TAAAGAAGAA 0.667082 -13 ATAGGACTAAATATGACCAATTTTAGATTA 7 51 0 ATATGACCAA 0.734262 -234 CAAACATATTATATGAAGAAAGGTATTTTC 7 102 1 ATATGAAGAA 0.944632 -183 TTCTTGATTTTTATCAAAAATCAATCTTTA 7 141 0 TTATCAAAAA 0.849046 -144 TTTTTGATAAAAATCAAGAAATAAAAACTA 7 151 1 AAATCAAGAA 0.970576 -134 AATACAGAAAATAATAAGAATAGTTTTTAT 7 171 0 ATAATAAGAA 0.652638 -114 CTACAACTACTAATCAACAATCAACGGCTC 7 226 0 TAATCAACAA 0.84719 -59 ********** Masking position 6 Map Score: 6.66219 Number of sites scoring better than the average of aligned sites = 917 Number in coding regions = 771 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 3 TTTTCCCTAAAATCGGCTAGAATACGCCGATT 3 65 1 AATCGCTAGA 0.910899 -42 AACAAAGCATAATTGGCAACTAGGATTAGCAA 4 143 1 AATTGCAACA 0.941838 -110 TGGCAACTAGGATTAGCAAGCATATTGTCGCC 4 156 1 GATTGCAAGA 0.990913 -97 GTGTGTTTTTGATTTGCCAAAACAGCCTGATC 4 196 1 GATTGCCAAA 0.867861 -57 AAAACAGCCTGATCTTCAAGAAAAAATTGAAG 4 214 1 GATCTCAAGA 0.973946 -39 TAAATTTGAAGATTTTCAAGTAACTACT 6 15 1 GATTTCAAGA 0.982289 -18 AGCATAACGGAATAGGCAAGCACGTTTAATCT 7 25 1 AATAGCAAGA 0.973601 -260 AAATAATAATAATTCTCAAACATATTATATGA 7 86 1 AATTTCAAAA 0.907998 -199 GATTTTTGATAAAAATCAAGAAATAAAAACTA 7 149 1 AAAATCAAGA 0.74742 -136 **** ***** * Masking position 9 Map Score: 5.39818 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 214 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TTCAGTCTTAAGCCCTCCAATTCCCTCCTA 4 42 1 AGCCCTCCAA 0.989136 -211 TTGCCGTTAGCCCAAGCATAACGGAATA 7 9 1 AGCCCAAGCA 0.970898 -276 GGTGGGCTAAAGCCCACCCTACAACTACTA 7 244 0 AGCCCACCCT 0.992922 -41 GGTGGGCTTTAGCCCACCAAAAAACAATCG 7 256 1 AGCCCACCAA 0.995672 -29 ********** Masking position 1 Map Score: 3.34296 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 24 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 GGGAAAATTGACAGCGAAAAGGAAATTAAG 3 42 0 ACAGCGAAAA 0.896471 -65 TTGTAAGTCACCGAAAATAAAATCGGCGT 3 88 0 ACCGAAAATA 0.825078 -19 TAATCATTTCACACCCAGTATACTGGGTGT 4 90 1 ACACCCAGTA 0.961472 -163 AGAGAGTACAACACCCAGTATACTGGGTGT 4 100 0 ACACCCAGTA 0.961472 -153 TACTCTCTGTAAAGAGAGTACAACACCCAG 4 112 0 AAAGAGAGTA 0.902466 -141 TACTCTCTTTACAGAGAGTACAACAAAGCA 4 122 1 ACAGAGAGTA 0.986175 -131 AGGTTTAAATACAGAAAATAATAAGAATAG 7 178 0 ACAGAAAATA 0.938761 -107 ********** Masking position 7 Map Score: 3.01966 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 114 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TCAGTCTTAAGCCCTCCAATTCCCTCCTAA 4 43 1 GCCCTCCAAT 0.984929 -210 GCCCTCCAATTCCCTCCTAATTAAATAGTT 4 53 1 TCCCTCCTAA 0.959299 -200 GTGGGCTAAAGCCCACCCTACAACTACTAA 7 243 0 GCCCACCCTA 0.98212 -42 GTGGGCTTTAGCCCACCAAAAAACAATCGA 7 257 1 GCCCACCAAA 0.99398 -28 ********** Masking position 6 Map Score: 1.39368 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 33 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TAATTGCTCCTTTTTTATATACA 1 47 0 TTGCTCCTTT 0.967296 -13 GTGAGCAATTTTGATCACTTTCTGCCA 4 8 0 TTGATCACTT 0.978642 -245 GTGATCAAAATTGCTCACTTTTTTCAGTCT 4 20 1 TTGCTCACTT 0.986087 -233 AGTTCAATTTTTAATCATTTCACACCCAGT 4 79 1 TTAATCATTT 0.890517 -174 TAATCTAAAATTGGTCATATTTAGTCCTAT 7 51 1 TTGGTCATAT 0.915567 -234 ********** Masking position 5 Map Score: 1.1881 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 86 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 ********** No masking Map Score: 1.41641e-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: 1.41641e-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: 1.41641e-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