AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 obg 85 obg #2 rplU 300 rplU Motif number 1 AGTGGGCGCACACGCGCGACGC 1 2 0 CACGCGCACG 0.963461 -84 CGCGCGTGTGCGCCCACTGCGAAGATTCACG 1 15 1 CGCCCACGCG 0.982573 -71 GCGGAGTGTGCAGCTACTGCGGGTTTTGCCC 1 48 0 CAGCTACGCG 0.907708 -38 AGCTCCCCTTCATCTGCGGAGTGTGCAGCTA 1 63 0 CATCTGCGAG 0.866676 -23 GCCGCAGCCATCAGCGGTCCAACCCG 2 6 1 AGCCATCGCG 0.970039 -295 CGGGTGGTGACGTCATCCGGGTTGGACCGCT 2 23 0 CGTCATCGGG 0.983406 -278 CGGATGACGTCACCACCCGGGCCCCGGAGTG 2 35 1 CACCACCGGG 0.977964 -266 ACGCTACCGGCGCACTCCGGGGCCCGGGTGG 2 47 0 CGCACTCGGG 0.964992 -254 CCGGTAGCGTCGAGATCGACGCTACCGGCGC 2 68 1 CGAGATCACG 0.900818 -233 GGGGCCTCAGCGAGATCGACGCCAGCACACG 2 104 0 CGAGATCACG 0.900818 -197 TACGGGGTCAAACCAGCGGGGCCTCAGCGAG 2 121 0 AACCAGCGGG 0.96398 -180 ACGTGACCTGCAACTACGGGGTCAAACCAGC 2 135 0 CAACTACGGG 0.951116 -166 GTCAGCCTGGCGACAACTGGTCAAGGGTACG 2 163 0 CGACAACGGT 0.775166 -138 CGTCTCCAGCCGTCAGCCTGGCGACAACTGG 2 174 0 CGTCAGCTGG 0.90184 -127 CTTGGGCGGGCACCTACAACGGACCCCGCAT 2 205 0 CACCTACACG 0.958012 -96 AGCGGCGGGACGCGTGCTGGGTCTTGGGCGG 2 227 0 CGCGTGCGGG 0.995775 -74 TTCGCGCGCGGGCCAGCGGCGGGACGCGTGC 2 241 0 GGCCAGCGCG 0.985187 -60 GCCGCTGGCCCGCGCGCGAAGCGCAACGCAT 2 252 1 CGCGCGCAAG 0.917264 -49 CGAAGCGCAACGCATGCAGCGGAAGTATGAA 2 268 1 CGCATGCGCG 0.985899 -33 ******* *** Masking position 7 Map Score: 32.344 Number of sites scoring better than the average of aligned sites = 42998 Number in coding regions = 40460 Number in noncoding regions = 2538 Number of orfs with sites within 600 bp upstream = 1174 Fraction of orfs with sites within 600 bp upstream = 0.188564 Motif number 2 GCGTCGCGCGTGTGCGCCCACTGCGAAGA 1 9 1 CGTGTGCCCC 0.996312 -77 TCATCTGCGGAGTGTGCAGCTACTGCGGGTT 1 54 0 AGTGTGCGCT 0.981947 -32 ACCCGGATGACGTCACCACCCGGGCCCCGGA 2 32 1 CGTCACCCCC 0.967163 -269 CGGGCCCCGGAGTGCGCCGGTAGCGTCGAGA 2 52 1 AGTGCGCGGT 0.977963 -249 AGCACACGAAAGTGCGCCGGTAGCGTCGATC 2 81 0 AGTGCGCGGT 0.977963 -220 GGCGCACTTTCGTGTGCTGGCGTCGATCTCG 2 94 1 CGTGTGCGGC 0.997495 -207 GTCAAGGGTACGTGACCTGCAACTACGGGGT 2 144 0 CGTGACCGCA 0.979648 -157 GACCCCGCATCGTCTCCAGCCGTCAGCCTGG 2 184 0 CGTCTCCGCC 0.994899 -117 GTCCGTTGTAGGTGCCCGCCCAAGACCCAGC 2 212 1 GGTGCCCCCC 0.978331 -89 AGACCCAGCACGCGTCCCGCCGCTGGCCCGC 2 234 1 CGCGTCCGCC 0.993955 -67 CGTTGCGCTTCGCGCGCGGGCCAGCGGCGGG 2 249 0 CGCGCGCGGC 0.995473 -52 CCTCTTCATACTTCCGCTGCATGCGTTGCGC 2 272 0 CTTCCGCGCA 0.858921 -29 ******* *** Masking position 7 Map Score: 26.7034 Number of sites scoring better than the average of aligned sites = 9432 Number in coding regions = 8750 Number in noncoding regions = 682 Number of orfs with sites within 600 bp upstream = 542 Fraction of orfs with sites within 600 bp upstream = 0.0870543 Motif number 3 TCGTGAATCTTCGCAGTGGGCGCACACGCG 1 17 0 TCGCAGTGGG 0.927789 -69 GGGGCAAAACCCGCAGTAGCTGCACACTCC 1 47 1 CCGCAGTAGC 0.945997 -39 GGACCGCTGATGGCTGCGGC 2 1 0 TGGCTGCGGC 0.990932 -300 GGGGCCCGGGTGGTGACGTCATCCGGGTTG 2 30 0 TGGTGACGTC 0.724424 -271 CGGAGTGCGCCGGTAGCGTCGAGATCGACG 2 59 1 CGGTAGCGTC 0.992356 -242 GAAAGTGCGCCGGTAGCGTCGATCTCGACG 2 75 0 CGGTAGCGTC 0.992356 -226 CACTTTCGTGTGCTGGCGTCGATCTCGCTG 2 98 1 TGCTGGCGTC 0.877604 -203 GGCGTCGATCTCGCTGAGGCCCCGCTGGTT 2 112 1 TCGCTGAGGC 0.914628 -189 TGGTTTGACCCCGTAGTTGCAGGTCACGTA 2 137 1 CCGTAGTTGC 0.81807 -164 ACAACGGACCCCGCATCGTCTCCAGCCGTC 2 191 0 CCGCATCGTC 0.957623 -110 TTCGCGCGCGGGCCAGCGGCGGGACGCGTG 2 242 0 GGCCAGCGGC 0.949913 -59 CTTCATACTTCCGCTGCATGCGTTGCGCTT 2 270 0 CCGCTGCATG 0.811312 -31 ********** Masking position 10 Map Score: 13.145 Number of sites scoring better than the average of aligned sites = 50170 Number in coding regions = 47259 Number in noncoding regions = 2911 Number of orfs with sites within 600 bp upstream = 1198 Fraction of orfs with sites within 600 bp upstream = 0.192419 Motif number 4 AGCTACTGCGGGTTTTGCCCCTCGTGAATCT 1 37 0 GGTTTGCCCC 0.951552 -49 ACGTCATCCGGGTTGGACCGCTGATGGCTGC 2 14 0 GGTTGACCGC 0.992152 -287 CGTCGATCTCGCTGAGGCCCCGCTGGTTTGA 2 114 1 GCTGGGCCCC 0.94933 -187 AGGCCCCGCTGGTTTGACCCCGTAGTTGCAG 2 128 1 GGTTGACCCC 0.95369 -173 GCTGGGTCTTGGGCGGGCACCTACAACGGAC 2 212 0 GGGCGGCACC 0.920069 -89 **** ****** Masking position 8 Map Score: 5.15463 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 625 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 CCACTGCGAAGATTCACGAGGGGCAAAACC 1 28 1 GATTCACGAG 0.822465 -58 ACACTCCGCAGATGAAGGGGAGCTCG 1 70 1 GATGAAGGGG 0.972814 -16 GGCGCACTCCGGGGCCCGGGTGGTGACGTC 2 40 0 GGGGCCCGGG 0.900565 -261 TGACCCCGTAGTTGCAGGTCACGTACCCTT 2 142 1 GTTGCAGGTC 0.943364 -159 GGCTGGAGACGATGCGGGGTCCGTTGTAGG 2 194 1 GATGCGGGGT 0.959243 -107 TGCGGGGTCCGTTGTAGGTGCCCGCCCAAG 2 206 1 GTTGTAGGTG 0.84025 -95 GCGCGGGCCAGCGGCGGGACGCGTGCTGGG 2 237 0 GCGGCGGGAC 0.902342 -64 AAGCGCAACGCATGCAGCGGAAGTATGAAG 2 270 1 CATGCAGCGG 0.871175 -31 GAAGTATGAAGAGGCAGGAGCA 2 289 1 GAGGCAGGAG 0.992239 -12 ********** Masking position 4 Map Score: 2.18528 Number of sites scoring better than the average of aligned sites = 13500 Number in coding regions = 12661 Number in noncoding regions = 839 Number of orfs with sites within 600 bp upstream = 604 Fraction of orfs with sites within 600 bp upstream = 0.0970125 Motif number 6 ********** No masking Map Score: 8.19556e-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 7 ********** No masking Map Score: 8.19556e-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: 8.19556e-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