AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_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 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 GTGAAAAATGACCGCACTTTTTGTTGATTA 1 51 0 ACCGCACTTT 0.999071 -250 GTCATTTTTCACCGCACTTTTTACCTGTTA 1 69 1 ACCGCACTTT 0.999071 -232 TGCTGATTATACCGAAATTTAGGCGTTTTT 1 250 0 ACCGAAATTT 0.975644 -51 TTCATTTTCAACCGCACTTTACACACCAAA 6 20 1 ACCGCACTTT 0.999071 -47 CTAAAAAATAACCGCACTTTGGTGTGTAAA 6 37 0 ACCGCACTTT 0.999071 -30 ********** Masking position 6 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 0.978888 -216 TATTTGAGCAGCTATTTGATTTAGCAAAAT 1 103 0 GCTATTTGAT 0.989142 -198 CCCACTCTTAGCTATTTGAGCAGCTATTTG 1 115 0 GCTATTTGAG 0.988398 -186 TTTTGAGTAGGCGATTTCATAAAGAAAGTA 1 197 0 GCGATTTCAT 0.889092 -104 TTTTGCTTTTTGATTTAGTTCTCA 4 5 1 GCTTTTTGAT 0.927631 -31 TCATTTAACTGATATTTTATCAAGCTAAAA 5 20 1 GATATTTTAT 0.898346 -273 CGCGTATAGCGGTATTTTAGCTTGATAAAA 5 34 0 GGTATTTTAG 0.924524 -259 GAGGCATCCAGCTGTTTTAGGTCAAATTTA 5 64 0 GCTGTTTTAG 0.917636 -229 AAATTCGAAAGTGATTTGAGAATATAGCTT 5 233 0 GTGATTTGAG 0.943318 -60 CCAAAGTGCGGTTATTTTTTAGGATAAATT 6 45 1 GTTATTTTTT 0.786977 -22 TCTTGAGCGGTTATTTTATAGAATAAGCC 8 38 0 GTTATTTTAT 0.96675 -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 GCAGCTATTTGATTTAGCAAAATCAAATAACA 1 94 0 GATTAGCAAA 0.862739 -207 AAAGAATGATTATTTAGCCAATTTCAGGTATT 1 151 0 TATTAGCAAT 0.80919 -150 CAGCACAATTTTTTAAGAAAAACAGGATTGTT 1 275 1 TTTAAGAAAA 0.96236 -26 ACTGATATTTTATCAAGCTAAAATACCGCTAT 5 27 1 TATAAGCAAA 0.9754 -266 CATCCAGCTGTTTTAGGTCAAATTTACGCGTA 5 58 0 TTTAGGTAAA 0.766295 -235 ATTTTATACTTTTCAAGCAAAATTGCAAGTTT 5 164 0 TTTAAGCAAA 0.985113 -129 TTTCTCTGTATATATAGACAAAAAGCCTGCGA 5 196 0 TATTAGAAAA 0.934015 -97 TGCGGTTATTTTTTAGGATAAATTTG 6 51 1 TTTAGGAAAA 0.913017 -16 TTATACGATATTTATAGCTAAAAATAAAACGC 7 23 0 TTTTAGCAAA 0.981859 -63 TAAGCCAATTTTTTAAGCCAGAAGGAAAAAAC 8 12 0 TTTAAGCAGA 0.926827 -45 GAGCGGTTATTTTATAGAATAAGCCAATTTTT 8 31 0 TTTTAGATAA 0.753988 -26 *** **** *** Masking position 3 Map Score: 9.94021 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 282 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 4 TTTGTTGATTAACGAACAAAAGGATTTTCCCT 1 30 0 ACGACAAAAG 0.706869 -271 TTGTTCGTTAATCAACAAAAAGTGCGGTCATT 1 43 1 ACAAAAAAAG 0.911512 -258 AAATCAAATAACAGGTAAAAAGTGCGGTGAAA 1 75 0 AAGGAAAAAG 0.976533 -226 AGTATAGGACATAAGGAAAAAGAATGATTATT 1 169 0 AAAGAAAAAG 0.962867 -132 CACAATTTTTTAAGAAAAACAGGATTGTTAGC 1 278 1 TAGAAAACAG 0.817176 -23 GTTTGAGAACTAAATCAAAAAGCAAAA 4 6 0 TAATAAAAAG 0.570331 -30 CTCGTATTATATCGTAAAACAAAATAAATTGT 5 91 1 ACGTAAACAA 0.62059 -202 ATGATAATTAAAAGGAATACAACCTACTTTAT 5 125 1 AAGGATACAA 0.709723 -168 ATTTTGCTTGAAAAGTATAAAATTCGCAGGCT 5 173 1 AAAGATAAAA 0.696759 -120 CTCTGTATATATAGACAAAAAGCCTGCGAATT 5 193 0 AAGAAAAAAG 0.972916 -100 GTCTATATATACAGAGAAAAAAGTAAGCTATA 5 209 1 AAGAAAAAAA 0.94433 -84 ATTTATAGCTAAAAATAAAACGCACTCAATAT 7 14 0 AAAAAAAACG 0.765549 -72 ATACCTTACAAAAAATAAACAAATAAAATCTA 7 60 0 AAAAAAACAA 0.875138 -26 TTTTTAAGCCAGAAGGAAAAAACA 8 3 0 AAAGAAAAAA 0.924497 -54 * *** ****** Masking position 9 Map Score: 7.99829 Number of sites scoring better than the average of aligned sites = 1044 Number in coding regions = 749 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 5 AAGTGCGGTGAAAAATGACCGCACTTTTTG 1 58 0 AAAAATGACC 0.970776 -243 AATAATACCTGAAATTGGCTAAATAATCAT 1 148 1 GAAATTGGCT 0.939218 -153 CATTTCAAATGAAAATGACTTTTTGAGTAG 1 217 0 GAAAATGACT 0.961963 -84 CTATACGCGTAAATTTGACCTAAAACAGCT 5 55 1 AAATTTGACC 0.883456 -238 AGTGATTTGAGAATATAGCTTACTTTTTTC 5 224 0 GAATATAGCT 0.780081 -69 ATTTATCCTAAAAAATAACCGCACTTTGGT 6 44 0 AAAAATAACC 0.928492 -23 TCTGGCTTAAAAAATTGGCTTATTCTATAA 8 22 1 AAAATTGGCT 0.927515 -35 GCTTATTCTATAAAATAACCGCTCAAGA 8 39 1 TAAAATAACC 0.797841 -18 ********** Masking position 3 Map Score: 4.54569 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 388 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 ********** 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 7 ********** 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 8 ********** 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