AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i337_weak_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 HI1250 300 H. influenzae predicted coding region HI1250 #2 HI1252 162 ABC transporter, ATP-binding protein #3 HI1603 207 conserved hypothetical protein #4 HI1604 24 phosphate permease, putative #5 HI1605 65 conserved hypothetical protein Motif number 1 AGGGAAATGCTATTGAGAGTTTTTTTGATTTACATCAA 1 66 0 TGTTTTTTGA 0.994234 -235 TTAGCTATATTTATCATTATTTTATTTAGGAACTTTAT 1 156 0 TCTTTTTTTA 0.971421 -145 TGCCACCCGTTTCGGGTGGTTTTTTTTATCTAAGTCGA 1 204 1 TGTTTTTTTA 0.971428 -97 TCCAGTAGAATAGGGCGAATTTTTTTGTGAGGAATTAT 2 133 1 TGTTTTTTGT 0.982001 -30 AAACCTTTTTTCTTACAAATTTTTTTGAAAAATTTTAA 3 115 1 TATTTTTTGA 0.96948 -93 CGTGCGCATATTACCCGATTTTTGTTGATAGTTAAAAT 3 146 0 TCTTTTTTGA 0.994236 -62 AGTTTATTTCCTATGTTTTGTTGA 4 1 0 TCTTTTTTGA 0.994242 -24 GGTTAAAATTAACCGCACTTTTTATTGAGATCAA 5 7 0 AGTTTTTTGA 0.964563 -59 CGGTTAATTTTAACCGCACTTTTGTTGTGATGTTTAAG 5 30 1 TCTTTTTTGT 0.981996 -36 * * **** **** Masking position 10 Map Score: 13.9457 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 56 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 GCAAAAACGAATTTTTCTGTCAAAAATGTTGAT 1 38 1 ATTTCTTCAA 0.975342 -263 ATAGCATTTCCCTTGCCTTTCAATATTCAGTAA 1 91 1 CCTTCTTCAA 0.942033 -210 TTTGAGCCCTAAAGTGTCTATTT 2 1 1 TTTGCCTAAA 0.861986 -162 TTTAGGGAATACTTCACTCTAAATATTTACAAG 2 36 1 ACTTCTTAAA 0.907752 -127 TTTTTTACCTTTCAAATTTTCTCGC 3 3 1 TTTTCTTCAA 0.990821 -205 CTCAATACACTTTTCGCTTTAAAAGCGAGAAAA 3 27 0 TTTTCTTAAA 0.978952 -181 AAGATAAACCTTTTTTCTTACAAATTTTTTTGA 3 110 1 TTTTCTACAA 0.944308 -98 TTTTGAAAAATTTTAACTATCAACAAAAATCGG 3 137 1 TTTTCTTCAA 0.990609 -71 TTTTTCCCCTTAAACATCACAACA 5 52 0 TTTTCCTAAA 0.963861 -14 **** ** **** Masking position 3 Map Score: 10.206 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 120 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 TATTGAGAGTTTTTTTGATTTACATCAACAT 1 63 0 TTTTTGATTT 0.922452 -238 CGTCAAGTGATTGCTTGATATTCATAAAGTT 1 133 1 TTGTTGATAT 0.896161 -168 GCATTGTGCATTTATTCTTATTATGATCAGC 1 255 1 TTTTTCTTAT 0.770235 -46 TAGGGCGAATTTTTTTGTGAGGAATTATTA 2 143 1 TTTTTGTGAG 0.947896 -20 AAGCGAAAAGTGTATTGAGTTACTTATCTTA 3 41 1 TGTTTGAGTT 0.833648 -167 TTACCCGATTTTTGTTGATAGTTAAAATTTT 3 143 0 TTTTTGATAG 0.948453 -65 AACCGCACTTTTTATTGAGATCAA 5 4 0 TTTTTGAGAT 0.980966 -62 TAACCGCACTTTTGTTGTGATGTTTAAGGGG 5 40 1 TTTTTGTGAT 0.969813 -26 *** ******* Masking position 6 Map Score: 5.3143 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 209 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 4 AATAATGATAAATATAGCTAAACTACTTTCC 1 173 1 AATATGCTAA 0.929415 -128 GTGTCTATTTAATTTAGGGAATACTTCACTC 2 24 1 AATTTGGGAA 0.966379 -139 ATTTTGCAAAAGTTTGGCGAAACCTAACCAC 2 68 0 AGTTTGCGAA 0.92873 -95 CAAGTGGACAGATTTTGCAAAAGTTTGGCGA 2 79 0 GATTTGCAAA 0.891489 -84 ATAGGGCGAAAATATAGGAAACAAGTGGACA 2 100 0 AATATGGAAA 0.957129 -63 TCTACTGGAAAATAGGGCGAAAATATAGGAA 2 111 0 AATAGGCGAA 0.971088 -52 TTTCCAGTAGAATAGGGCGAATTTTTTTGTG 2 131 1 AATAGGCGAA 0.971088 -32 TGATAGTTAAAATTTTTCAAAAAAATTTGTA 3 128 0 AATTTTCAAA 0.775139 -80 TCAACAAAACATAGGAAATAAACT 4 8 1 AACATGGAAA 0.839131 -17 ***** ***** Masking position 10 Map Score: 6.01673 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 482 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 AAATATTTACAAGTGGTTAGGTTTCGCCAA 2 56 1 AAGTGGTTAG 0.949844 -107 ATATTTCCTAGTGTGGTAAGATAAGTAACT 3 58 0 GTGTGGTAAG 0.941038 -150 ACTCCAAATTAAGGGGTTAAAAATTCGTGC 3 179 0 AAGGGGTTAA 0.972478 -29 TCAATAAAAAGTGCGGTTAATTTTAACCGC 5 17 1 GTGCGGTTAA 0.98232 -49 CACAACAAAAGTGCGGTTAAAATTAACCGC 5 29 0 GTGCGGTTAA 0.98232 -37 TGTGATGTTTAAGGGGAAAAA 5 55 1 AAGGGGAAAA 0.823696 -11 ********** Masking position 9 Map Score: 2.59352 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 301 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 6 TGAAGTTGTTTATTCTACACGCAAAAACGAATTTTTCTG 1 18 1 TTCTACAAAG 0.994648 -283 CGCAAAAACGAATTTTTCTGTCAAAAATGTTGATGTAAA 1 37 1 ATTTTCAAAG 0.89249 -264 GTGGTTTTTTTTATCTAAGTCGAAAGATGCACTCTTGCA 1 219 1 TTCTAAAAAG 0.967051 -82 AAATTCGCCCTATTCTACTGGAAAATAGGGCGAAAATAT 2 116 0 TTCTACAAAG 0.994753 -47 GAAAAAAGGTTTATCTTCGACTAAGTAAGCAACTGGGTA 3 88 0 TTCTTCAAAG 0.990196 -120 AAGTGATTTACTCCAAATTAAGGGGTTAAAAA 3 186 0 TTTTACAAAG 0.984644 -22 * ***** ** * * Masking position 13 Map Score: 2.39528 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 26 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 ********** No masking Map Score: -3.31523e-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: -3.31523e-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: -3.31523e-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