AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_mtub_reg_100.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 lepB 57 lepB #2 rplS 300 rplS #3 rpsP 183 rpsP #4 ffh 77 ffh Motif number 1 TTCGAAAGCCGCCACCTGCGCTGGCTACGCT 1 31 1 GCACCTGCGC 0.991871 -27 ATGACTAGGGTCAAACCGCGCGTGTGGAAAC 2 36 0 TAAACCGCGC 0.867913 -265 GGCGCTTTTCGACGGCCGCGAACCACCGGAG 2 92 1 GCGGCCGCGA 0.98178 -209 CACCGCGACAGACAACTGCTCAATTGTGCCA 2 155 0 GCAACTGCTC 0.932646 -146 CAACCCGGCCGACCACCGCGACAGACAACTG 2 168 0 GCCACCGCGA 0.996646 -133 CAGGCGGCACGCAACCCGGCCGACCACCGCG 2 179 0 GAACCCGGCC 0.839623 -122 GTTGCGTGCCGCCTGCTGCGAGATGCACCAA 2 195 1 GCTGCTGCGA 0.870267 -106 CCGGCTTGGTGACCACCGCACGCTGCGTGTG 2 240 1 GCCACCGCAC 0.973517 -61 GCGTGTGGGGGGTAACCACGCCGCGACCCCA 2 264 1 GTAACCACGC 0.920378 -37 AGCCCGCTGGGCGAATTACTGC 3 2 1 GCCGCTGGGC 0.5224 -182 ATTGGCGGCTGTCCACCGCGCGACGACTTGT 3 55 1 GCCACCGCGC 0.980712 -129 ACCACCGGGCGGCAACCCCGAACAGGACAAG 3 81 0 GCAACCCCGA 0.953736 -103 TCGCGTGTATGACCACCGGGCGGCAACCCCG 3 92 0 GCCACCGGGC 0.9096 -92 CTGCAATTCAGCGACCCGGGCGGGATGCCCG 3 137 0 GGACCCGGGC 0.975691 -47 TTGACTCTGCGTCCACCACGCAAAA 4 5 0 GCCACCACGC 0.994989 -73 TGGTGATCGCGAGCGCCGCGCAGCGGCACCG 4 43 0 GGCGCCGCGC 0.84039 -35 GCCCGCCAGCCTAATGGTGAT 4 67 0 GCCGCCAGCC 0.654872 -11 * ********* Masking position 6 Map Score: 39.6881 Number of sites scoring better than the average of aligned sites = 14368 Number in coding regions = 13352 Number in noncoding regions = 1016 Number of orfs with sites within 600 bp upstream = 704 Fraction of orfs with sites within 600 bp upstream = 0.113074 Motif number 2 GGAACGTCTCGGCGATGTTCGAAAGCCGCC 1 14 1 GGCGATGTTC 0.698191 -44 CAGCGCAGGTGGCGGCTTTCGAACATCGCC 1 24 0 GGCGGCTTTC 0.978081 -34 TGTTGGGTGTCACGCCAAGCTTCGG 2 6 1 GGTGTCACGC 0.975114 -295 ACCATTTGCGGGCGCTTTTCGACGGCCGCG 2 82 1 GGCGCTTTTC 0.899959 -219 GGAAATCTCCGGTGGTTCGCGGCCGTCGAA 2 99 0 GGTGGTTCGC 0.98452 -202 AATTGTGCCAGACGGTACGCATGCAGTGAA 2 135 0 GACGGTACGC 0.924212 -166 CAATTGAGCAGTTGTCTGTCGCGGTGGTCG 2 160 1 GTTGTCTGTC 0.474159 -141 TGTCTGTCGCGGTGGTCGGCCGGGTTGCGT 2 172 1 GGTGGTCGGC 0.883913 -129 TCTCGCAGCAGGCGGCACGCAACCCGGCCG 2 188 0 GGCGGCACGC 0.997082 -113 CGGGCTTATTGGTGCATCTCGCAGCAGGCG 2 204 0 GGTGCATCTC 0.673349 -97 ACACGCAGCGTGCGGTGGTCACCAAGCCGG 2 240 0 TGCGGTGGTC 0.718001 -61 GGGTAACCACGCCGCGACCCCAAGGATGGT 2 273 1 GCCGCGACCC 0.676278 -28 TGGCACAATTGGCGGCTGTCCACCGCGCGA 3 48 1 GGCGGCTGTC 0.981008 -136 AACAGGACAAGTCGTCGCGCGGTGGACAGC 3 62 0 GTCGTCGCGC 0.929868 -122 ATGACCACCGGGCGGCAACCCCGAACAGGA 3 85 0 GGCGGCAACC 0.846628 -99 CAGCGACCCGGGCGGGATGCCCGGATCCGG 3 130 0 GGCGGGATGC 0.96553 -54 CGCTCCTATTGGTGTCACGCTGCAATTCAG 3 157 0 GGTGTCACGC 0.975114 -27 GGATAACGGTGCCGCTGCGCGGCGCTCGCG 4 37 1 GCCGCTGCGC 0.958469 -41 TCACCATTAGGCTGGCGGGC 4 68 1 GCTGGCGGGC 0.938911 -10 ********** Masking position 4 Map Score: 24.5654 Number of sites scoring better than the average of aligned sites = 30149 Number in coding regions = 27909 Number in noncoding regions = 2240 Number of orfs with sites within 600 bp upstream = 1105 Fraction of orfs with sites within 600 bp upstream = 0.177482 Motif number 3 GGTGTCACGCCAAGCTTCGGGTTTCCACACG 2 16 1 CAGCTTCGGG 0.886278 -285 AGGGTCAAACCGCGCGTGTGGAAACCCGAAG 2 30 0 CGGCGTGTGG 0.737022 -271 GTCATGTGTACCATTTGCGGGCGCTTTTCGA 2 73 1 CCTTTGCGGG 0.804904 -228 GGTGGTCGGCCGGGTTGCGTGCCGCCTGCTG 2 182 1 CGGTTGCGTG 0.959423 -119 TTGCGTGCCGCCTGCTGCGAGATGCACCAAT 2 196 1 CCGCTGCGAG 0.956901 -105 CCGGTGGGTTCGGGCTTATTGGTGCATCTCG 2 213 0 CGGCTTATTG 0.547039 -88 CCCGAACCCACCGGCTTGGTGACCACCGCAC 2 230 1 CCGCTTGGTG 0.980605 -71 GTGACCACCGCACGCTGCGTGTGGGGGGTAA 2 248 1 CAGCTGCGTG 0.645524 -53 TGGAAATGACCATCCTTGGGGTCGCGGCGTG 2 280 0 CACCTTGGGG 0.858202 -21 AGCCCGCTGGGCGAATTACTGCC 3 3 1 CCGCTGGGCG 0.627362 -181 TGTGCCAGAACGTGATGCTGGGGCAGTAATT 3 24 0 CGGATGCTGG 0.850068 -160 GACGACTTGTCCTGTTCGGGGTTGCCGCCCG 3 76 1 CCGTTCGGGG 0.959636 -108 TTCGGGGTTGCCGCCCGGTGGTCATACACGC 3 90 1 CCCCCGGTGG 0.53973 -94 CGAGGCAAAACCGGATCCGGGCATCCCGCCC 3 120 1 CCGATCCGGG 0.948752 -64 TTCAGCGACCCGGGCGGGATGCCCGGATCCG 3 131 0 CGGCGGGATG 0.767959 -53 ATGGTGATCGCGAGCGCCGCGCAGCGGCACC 4 44 0 CGGCGCCGCG 0.888846 -34 ** ******** Masking position 1 Map Score: 21.236 Number of sites scoring better than the average of aligned sites = 18527 Number in coding regions = 17241 Number in noncoding regions = 1286 Number of orfs with sites within 600 bp upstream = 767 Fraction of orfs with sites within 600 bp upstream = 0.123193 Motif number 4 GCGTACCGTCTGGCACAATTGAGCAGTTGTC 2 145 1 TGGCCAATTG 0.996084 -156 AGCCCGCTGGGCGAATTACTGCCCCAGC 3 8 1 TGGGGAATTA 0.959808 -176 CATCACGTTCTGGCACAATTGGCGGCTGTCC 3 38 1 TGGCCAATTG 0.996084 -146 CCCGCCCGGGTCGCTGAATTGCAGCGTGACA 3 144 1 TCGCGAATTG 0.98957 -40 **** ****** Masking position 7 Map Score: 1.81005 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 23 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 ACAGACAACTGCTCAATTGTGCCAGACGGT 2 149 0 GCTCAATTGT 0.840257 -152 GTGGGTTCGGGCTTATTGGTGCATCTCGCA 2 211 0 GCTTATTGGT 0.978276 -90 TGGTCACCAAGCCGGTGGGTTCGGGCTTAT 2 225 0 GCCGGTGGGT 0.958239 -76 CGGGGTTGCCGCCCGGTGGTCATACACGCG 3 92 1 GCCCGGTGGT 0.985884 -92 GATTGAGCGCTCCTATTGGTGTCACGCTGC 3 164 0 TCCTATTGGT 0.952589 -20 GCCCGCCAGCCTAATGGTGATCGCGAGC 4 60 0 GCCTAATGGT 0.989292 -18 ********** Masking position 10 Map Score: 2.44346 Number of sites scoring better than the average of aligned sites = 1005 Number in coding regions = 924 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 GCGTAGCCAGCGCAGGTGGCGGCTTTCGAA 1 31 0 CGCAGGTGGC 0.946072 -27 GGTCAAACCGCGCGTGTGGAAACCCGAAGC 2 29 0 CGCGTGTGGA 0.985382 -272 GTGATTTCACTGCATGCGTACCGTCTGGCA 2 130 1 TGCATGCGTA 0.542634 -171 TCGGCCGGGTTGCGTGCCGCCTGCTGCGAG 2 187 1 TGCGTGCCGC 0.912022 -114 GTGGTCACCAAGCCGGTGGGTTCGGGCTTA 2 226 0 AGCCGGTGGG 0.865792 -75 CACCGCACGCTGCGTGTGGGGGGTAACCAC 2 253 1 TGCGTGTGGG 0.993379 -48 GACAAGTCGTCGCGCGGTGGACAGCCGCCA 3 57 0 CGCGCGGTGG 0.934554 -127 GGTTTTGCCTCGCGTGTATGACCACCGGGC 3 102 0 CGCGTGTATG 0.872615 -82 AATTCAGCGACCCGGGCGGGATGCCCGGAT 3 134 0 CCCGGGCGGG 0.821102 -50 TTTTGCGTGGTGGACGCAGAGTC 4 4 1 TGCGTGGTGG 0.959889 -74 ********** Masking position 3 Map Score: 6.55793 Number of sites scoring better than the average of aligned sites = 9199 Number in coding regions = 8344 Number in noncoding regions = 855 Number of orfs with sites within 600 bp upstream = 590 Fraction of orfs with sites within 600 bp upstream = 0.0947639 Motif number 7 ********** No masking Map Score: -1.07049e-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: -1.07049e-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: -1.07049e-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