AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_hinf_reg_100.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 HI0106 300 signal recognition particle protein (ffh) #2 HI0201 36 ribosomal protein L19 (rpL19) #3 HI0202 37 tRNA (guanine-N1)-methyltransferase (trmD) #4 HI0203 35 conserved hypothetical protein #5 HI0204 292 ribosomal protein S16 (rpS16) #6 HI1060 66 lipid-A-disaccharide synthetase (lpxB) #7 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #8 HI1064 56 conserved hypothetical protein Motif number 1 TAATCAACAAAAAGTGCGGTCATTTTTCAC 1 51 1 AAAGTGCGGT 0.998744 -250 TAACAGGTAAAAAGTGCGGTGAAAAATGAC 1 69 0 AAAGTGCGGT 0.998744 -232 AAAAACGCCTAAATTTCGGTATAATCAGCA 1 250 1 AAATTTCGGT 0.967127 -51 TTTGGTGTGTAAAGTGCGGTTGAAAATGAA 6 20 0 AAAGTGCGGT 0.998744 -47 TTTACACACCAAAGTGCGGTTATTTTTTAG 6 37 1 AAAGTGCGGT 0.998744 -30 ********** Masking position 5 Map Score: 16.2081 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 CTTTTTACCTGTTATTTGATTTTGCTAAAT 1 85 1 GTTATTTGAT 0.981948 -216 TATTTGAGCAGCTATTTGATTTAGCAAAAT 1 103 0 GCTATTTGAT 0.99073 -198 CCCACTCTTAGCTATTTGAGCAGCTATTTG 1 115 0 GCTATTTGAG 0.990094 -186 TTTTGAGTAGGCGATTTCATAAAGAAAGTA 1 197 0 GCGATTTCAT 0.90389 -104 TTTTGCTTTTTGATTTAGTTCTCA 4 5 1 GCTTTTTGAT 0.937647 -31 TCATTTAACTGATATTTTATCAAGCTAAAA 5 20 1 GATATTTTAT 0.912031 -273 CGCGTATAGCGGTATTTTAGCTTGATAAAA 5 34 0 GGTATTTTAG 0.93494 -259 GAGGCATCCAGCTGTTTTAGGTCAAATTTA 5 64 0 GCTGTTTTAG 0.928929 -229 AAATTCGAAAGTGATTTGAGAATATAGCTT 5 233 0 GTGATTTGAG 0.951277 -60 CCAAAGTGCGGTTATTTTTTAGGATAAATT 6 45 1 GTTATTTTTT 0.812526 -22 TCTTGAGCGGTTATTTTATAGAATAAGCC 8 38 0 GTTATTTTAT 0.971518 -19 ********** Masking position 5 Map Score: 14.0156 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 166 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 AGCAGCTATTTGATTTAGCAAAATCAAATAACA 1 94 0 TGATAGCAAA 0.914612 -207 AAAAGAATGATTATTTAGCCAATTTCAGGTATT 1 151 0 TTATAGCAAT 0.878529 -150 TCAGCACAATTTTTTAAGAAAAACAGGATTGTT 1 274 1 TTTTAGAAAA 0.902655 -27 AACTGATATTTTATCAAGCTAAAATACCGCTAT 5 26 1 TTATAGCAAA 0.982721 -267 ACAACCTACTTTATGCATACAAAACTTGCAATT 5 143 1 TTATATAAAA 0.697349 -150 AATTTTATACTTTTCAAGCAAAATTGCAAGTTT 5 164 0 TTTTAGCAAA 0.980633 -129 TTTTGTCTATATATACAGAGAAAAAAGTAAGCT 5 205 1 ATATAGAAAA 0.881304 -88 GTGCGGTTATTTTTTAGGATAAATTTG 6 50 1 TTTTGGAAAA 0.8681 -17 ATTATACGATATTTATAGCTAAAAATAAAACGC 7 23 0 ATTTAGCAAA 0.94377 -63 ATAAGCCAATTTTTTAAGCCAGAAGGAAAAAAC 8 12 0 TTTTAGCAGA 0.927155 -45 TGAGCGGTTATTTTATAGAATAAGCCAATTTTT 8 31 0 TTTTAGATAA 0.818019 -26 **** *** *** Masking position 4 Map Score: 11.0402 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 329 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 TTGTTGATTAACGAACAAAAGGATTTTCCCT 1 30 0 ACGACAAAAG 0.758426 -271 TTGTTCGTTAATCAACAAAAAGTGCGGTCAT 1 43 1 ATCACAAAAA 0.861932 -258 AAATCAAATAACAGGTAAAAAGTGCGGTGAA 1 76 0 ACAGTAAAAA 0.895988 -225 AGTATAGGACATAAGGAAAAAGAATGATTAT 1 170 0 ATAAGAAAAA 0.963924 -131 TTCATTTGAAATGATGAAAAACGCCTAAATT 1 234 1 ATGAGAAAAA 0.919929 -67 ATTGTGAATGATAATTAAAAGGAATACAACC 5 118 1 ATAATAAAAG 0.832361 -175 CTCTGTATATATAGACAAAAAGCCTGCGAAT 5 194 0 ATAGCAAAAA 0.961521 -99 GTCTATATATACAGAGAAAAAAGTAAGCTAT 5 209 1 ACAGGAAAAA 0.946785 -84 TACGATATTTATAGCTAAAAATAAAACGCAC 7 21 0 ATAGTAAAAA 0.923656 -65 CTTACAAAAAATAAACAAATAAAATCTATCG 7 57 0 ATAACAAATA 0.772469 -29 TTTTTAAGCCAGAAGGAAAAAACA 8 4 0 AGAAGAAAAA 0.876495 -53 **** ****** Masking position 7 Map Score: 7.46689 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 357 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 5 TTAATCAACAAAAAGTGCGGTCATTTTTCACCGCACT 1 50 1 AAAGTGTTTT 0.898781 -251 CGCCTACTCAAAAAGTCATTTTCATTTGAAATGATGA 1 214 1 AAAGTTATTT 0.615531 -87 TAAATTTCGGTATAATCAGCACAATTTTTTAAGAAAA 1 259 1 TAAATGATTT 0.972228 -42 AAAATATCAGTTAAATGAGGTTTATAT 5 1 0 TTAATGATAT 0.499156 -292 TGTTTTACGATATAATACGAGGCATCCAGCTGTTTTA 5 75 0 TAAATGATCC 0.786582 -218 TTTGTATGCATAAAGTAGGTTGTATTCCTTTTAATTA 5 129 0 TAAGTGATTC 0.969064 -164 TTGAAAAGTATAAAATTCGCAGGCTTTTTGTCTATAT 5 180 1 TAAATGCTTT 0.89106 -113 ATACAGAGAAAAAAGTAAGCTATATTCTCAAATCACT 5 217 1 AAAGTGATTC 0.925594 -76 CTTTACACACCAAAGTGCGGTTATTTTTTAGGATAAA 6 36 1 CAAGTGTTTT 0.839084 -31 GCTATATTGAGTGCGTTTTATTTTTAGCTATAA 7 7 1 TTAGTGATTT 0.926222 -79 ATAAATATCGTATAATCCGATAGATTTTATTTGTTTA 7 40 1 TAAATGATTT 0.972228 -46 GGTTATTTTATAGAATAAGCCAATTTTTTAAGCCAGA 8 22 0 TAAATGTTTT 0.933081 -35 ** *** * **** Masking position 4 Map Score: 5.48707 Number of sites scoring better than the average of aligned sites = 816 Number in coding regions = 513 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 6 ATCATTTCAAATGAAAATGACTTTTTGAGT 1 219 0 ATGAAAATGA 0.885977 -82 ACAAAATAAATTGTGAATGATAATTAAAAG 5 109 1 TTGTGAATGA 0.945964 -184 CGAAAGTGATTTGAGAATATAGCTTACTTT 5 228 0 TTGAGAATAT 0.946923 -65 ACTTTCGAATTTGAGAATATTCTTTTAGTA 5 251 1 TTGAGAATAT 0.946923 -42 TAAAGTGCGGTTGAAAATGAAGAAGTTTTA 6 11 0 TTGAAAATGA 0.962355 -56 ********** Masking position 6 Map Score: 1.13853 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 92 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CCTGTTATTTGATTTTGCTAAATCAAATAGC 1 92 1 GATTTTGCTA 0.929183 -209 ATAATACCTGAAATTGGCTAAATAATCATTC 1 149 1 AAATTGGCTA 0.952438 -152 TTTCTTAAAAAATTGTGCTGATTATACCGAA 1 264 0 AATTGTGCTA 0.929183 -37 GTATAGCGGTATTTTAGCTTGATAAAATATC 5 30 0 ATTTTAGCTG 0.806103 -263 CAAAACTTGCAATTTTGCTTGAAAAGTATAA 5 162 1 AATTTTGCTG 0.966323 -131 GTGATTTGAGAATATAGCTTACTTTTTTCTC 5 222 0 AATATAGCTA 0.860689 -71 CTGGCTTAAAAAATTGGCTTATTCTATAAAA 8 23 1 AAATTGGCTA 0.952438 -34 ********* * Masking position 9 Map Score: 0.993301 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 217 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 GACATAAGGAAAAAGAATGATTATTTAGCC 1 164 0 AAAAGAATGA 0.825033 -137 TTCTTTATGAAATCGCCTACTCAAAAAGTC 1 201 1 AATCGCCTAC 0.81814 -100 AAATGATGAAAAACGCCTAAATTTCGGTAT 1 242 1 AAACGCCTAA 0.94734 -59 AAAAAGCCTACTACATTACGT 3 27 0 AAAAGCCTAC 0.980537 -11 AACTAAATCAAAAAGCAAAA 4 1 0 AAAAGCAAAA 0.795519 -35 ATGATAATTAAAAGGAATACAACCTACTTT 5 125 1 AAAGGAATAC 0.824812 -168 ATTTTGCTTGAAAAGTATAAAATTCGCAGG 5 173 1 AAAAGTATAA 0.792441 -120 TATATAGACAAAAAGCCTGCGAATTTTATA 5 188 0 AAAAGCCTGC 0.960983 -105 TTTAATTACTAAAAGAATATTCTCAAATTC 5 257 0 AAAAGAATAT 0.745681 -36 ********** Masking position 2 Map Score: 3.2812 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 218 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 ********** No masking Map Score: 3.79592e-14 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: 3.79592e-14 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 11 ********** No masking Map Score: 3.79592e-14 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