AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i118_SecDF_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 HI0240 69 protein-export membrane protein (secD) #2 HI0241 107 conserved hypothetical protein #3 HI0243 64 H. influenzae predicted coding region HI0243 #4 HI0244 300 tRNA-guanine transglycosylase (tgt) Motif number 1 AATGCGTGGCTCTGGAAAATAATTTAATGTT 1 15 0 TTGGAAAATA 0.864164 -55 TGTGGCTCTGTGCGTTAGAAAAGAAAAGGAA 1 45 1 TCGTTAGAAA 0.946255 -25 TTAAAAATTTTGCGTAAAATACCATAAATTG 2 64 0 TCGTAAAATA 0.882636 -44 CTTATTAATTTAAGTTAAAAATTTTGCGTAA 2 78 0 TAGTTAAAAA 0.956894 -30 CTTAAATTAATAAGGAAAACACA 2 95 1 TAGGAAAACA 0.804314 -13 TTAATAAAAGTGCGGTAGAAAAATAAAACGT 3 11 1 TCGGTAGAAA 0.959426 -54 TGTTAAAAAGTGCGGTCAAAAAACGTTTTAT 3 33 0 TCGGTCAAAA 0.935047 -32 AAGATTTCCTTTGTTAAAAAGTGCGGTCAA 3 45 0 TTGTTAAAAA 0.957466 -20 TTAATCATACTAAGGATAAAAATATGACTAA 4 114 0 TAGGATAAAA 0.830245 -187 AACAAAAAAGCCTGTTAAAAAATACAGGCTT 4 243 0 CTGTTAAAAA 0.845019 -58 AACAGGCTTTTTTGTTTAAAAAATCTTCGAA 4 258 1 TTGTTTAAAA 0.889067 -43 * ********* Masking position 9 Map Score: 8.85515 Number of sites scoring better than the average of aligned sites = 1075 Number in coding regions = 792 Number in noncoding regions = 283 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 2 TTTCCAGAGCCACGCATTGTGGCTCTGTGC 1 28 1 CACGCATTGT 0.968987 -42 CGTAGGATATTGGGCTTAGTTCGCCTTTCC 2 26 1 TGGGCTTAGT 0.920623 -82 GTTTTTTGACCGCACTTTTTAACAAAGGAA 3 40 1 CGCACTTTTT 0.844888 -25 TTTTCAATAACAGGCAAAGTAGAATAATGA 4 64 1 CAGGCAAAGT 0.933391 -237 TTGCCGCTGTCGGGCTATTTCGTAGATCCT 4 152 0 CGGGCTATTT 0.977423 -149 TTAAAAAATACAGGCTTTGTGATATCATAT 4 230 0 CAGGCTTTGT 0.994159 -71 TATTTTTTAACAGGCTTTTTTGTTTAAAAA 4 250 1 CAGGCTTTTT 0.988011 -51 ********** Masking position 10 Map Score: 7.00725 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 217 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 GAAAAGTAGCACTGGCTATTAGTAGTTGAT 4 39 0 ACTGGCTATT 0.980007 -262 CTTTTCAATAACAGGCAAAGTAGAATAATG 4 63 1 ACAGGCAAAG 0.926287 -238 GTTGCCGCTGTCGGGCTATTTCGTAGATCC 4 153 0 TCGGGCTATT 0.95739 -148 GTTAAAAAATACAGGCTTTGTGATATCATA 4 231 0 ACAGGCTTTG 0.989535 -70 GTATTTTTTAACAGGCTTTTTTGTTTAAAA 4 249 1 ACAGGCTTTT 0.988156 -52 ********** Masking position 5 Map Score: 3.58871 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 67 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 ACAATGCGTGGCTCTGGAAAATAATTTAAT 1 18 0 GCTCTGGAAA 0.934943 -52 CGTTAGAAAAGAAAAGGAAAACT 1 57 1 GAAAAGGAAA 0.927152 -13 AACTTAAATTAATAAGGAAAACACA 2 93 1 AATAAGGAAA 0.966265 -15 GCACTTTTTAACAAAGGAAATCTT 3 51 1 ACAAAGGAAA 0.978463 -14 TGTTAATCATACTAAGGATAAAAATATGAC 4 117 0 ACTAAGGATA 0.978463 -184 TGATTAACAAACTCAGGATCTACGAAATAG 4 138 1 ACTCAGGATC 0.932167 -163 ********** Masking position 8 Map Score: 3.36859 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 79 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 GAATAACATTAAATTATTTTCCAGA 1 6 1 ACATTAAATT 0.936338 -64 TGCGTAAAATACCATAAATTGCTTCATTGG 2 55 0 ACCATAAATT 0.98456 -53 CAAAATTTTTAACTTAAATTAATAAGGAAA 2 83 1 AACTTAAATT 0.878121 -25 GACCAACTTAATCATAAATTTAGTCATATT 4 95 1 ATCATAAATT 0.959834 -206 ********** Masking position 5 Map Score: 1.58159 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 26 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 ATTGTGGCTCTGTGCGTTAGAAAAGAAAAG 1 43 1 TGTGCGTTAG 0.977171 -27 AGTTAAAAATTTTGCGTAAAATACCATAAA 2 67 0 TTTGCGTAAA 0.822107 -41 TTAATAAAAGTGCGGTAGAAAAATAAAA 3 9 1 AGTGCGGTAG 0.992841 -56 TTTGTTAAAAAGTGCGGTCAAAAAACGTTT 3 36 0 AGTGCGGTCA 0.982862 -29 GAGATGGCGGTAACCATCTCTTG 4 4 1 ATGGCGGTAA 0.96254 -297 ********** Masking position 5 Map Score: 1.38663 Number of sites scoring better than the average of aligned sites = 1610 Number in coding regions = 1108 Number in noncoding regions = 502 Number of orfs with sites within 600 bp upstream = 326 Fraction of orfs with sites within 600 bp upstream = 0.0523611 Motif number 7 ********** No masking Map Score: 1.42352e-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 8 ********** No masking Map Score: 1.42352e-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: 1.42352e-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