AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i221_Ribosomal_Operon_8_mthe_reg_100.orf -o221_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -x5 -e 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH00129 300 M.thermo #2 RTH02041 58 M.thermo #3 RTH01062 171 M.thermo #4 RTH01098 51 M.thermo #5 RTH00022 27 M.thermo Motif number 1 ATATTGACTGCAGCCCTGTTCCTTGTGGGCCTTTC 1 58 0 CACCGCCTTG 0.991005 -243 GTTTCATCCTCATCGGAGTGCCTGTTTATCTTGGA 1 94 0 CACGGCCTGT 0.99578 -207 AAGGTTTCCGCTTCCAAGGACCTTTCCAGGCACGA 1 134 0 CTCCGCCTTT 0.996147 -167 GACAGGGCAACAACCTGGACCCTGTGGTCAAGGTT 1 163 0 CACCGCCTGT 0.999186 -138 GTCAGGCACTCTCCCCCGGCCCTCTCGATCTTATC 1 217 0 CTCCGCCTCT 0.997506 -84 CGGTGCTGACCATCCCCGTTCCAGTTGAAAAGTCC 3 61 0 CACCGCCAGT 0.996092 -111 GAACTCGGGTCTCCAGCGTTCCGGTGCTGACCATC 3 82 0 CTCAGCCGGT 0.968295 -90 CATCAAATCGAATCCAAGAACCTCTATTTTAATGT 3 132 1 AACCGCCTCT 0.986235 -40 ** ** * ***** Masking position 8 Map Score: 14.763 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 203 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 CAGCCCTGTTCCTTGTGGGCCTTTCGAGTC 1 53 0 CCTTGTGGGC 0.86901 -248 ACAACCTGGACCCTGTGGTCAAGGTTTCCG 1 159 0 CCCTGTGGTC 0.993113 -142 CAGGTTGTTGCCCTGTCATTTTCACAGACA 1 181 1 CCCTGTCATT 0.948648 -120 CGATCTTATCCCTTGCTGTCTGTGAAAATG 1 197 0 CCTTGCTGTC 0.943184 -104 GGCACTCTCCCCCGGCCCTCTCGATCTTAT 1 218 0 CCCGGCCCTC 0.98995 -83 TTGAAGAGAACCCGGCCATTAAGAACATAA 1 266 1 CCCGGCCATT 0.981936 -35 GACCAAGCTACCCTACGGTCCC 3 3 0 CCCTACGGTC 0.977341 -169 GGTCCATCCTCCCAGCCATTGAAGAAGTTT 3 29 1 CCCAGCCATT 0.932862 -143 GAGTTCAAATCTCGGCGGTCCCATCAAATC 3 111 1 CTCGGCGGTC 0.976881 -61 ********** Masking position 1 Map Score: 10.6825 Number of sites scoring better than the average of aligned sites = 976 Number in coding regions = 918 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 AAGGACCTTTCCAGGCACGAGAACTGTTTCATCCTC 1 118 0 CCGCACGACG 0.991601 -183 AGGTTGTTGCCCTGTCATTTTCACAGACAGCAAGGG 1 182 1 CCGCATTACG 0.997467 -119 GGGGAGAGTGCCTGACACTCGGAAAAATTGTTGAAG 1 236 1 CCGCACTAAA 0.985954 -65 TGAAGAGAACCCGGCCATTAAGAACATAAAGATAAT 1 267 1 CCGCATTAAA 0.988327 -34 GTCCATCCTCCCAGCCATTGAAGAAGTTTCCGGACT 3 30 1 CCGCATTGAG 0.989204 -142 GAAGAAGTTTCCGGACTTTTCAACTGGAACGGGGAT 3 49 1 CCGCTTTACG 0.989815 -123 ** * **** ** * Masking position 6 Map Score: 4.75098 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 44 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 CATCCCAGGAAGGCGCAGCAATCTGGAA 1 7 1 AGGAAGGCAG 0.992238 -294 GCAATCTGGAAGGACGTTGCAAGGAGACTCGA 1 28 1 AGGACGTCAA 0.968581 -273 CACTCCGATGAGGATGAAACAGTTCTCGTGCC 1 109 1 AGGATGACAG 0.995233 -192 ACTAAAGAGTAGAATGATTCAGT 2 46 1 AGAATGACAG 0.975617 -13 AATGGCTGGGAGGATGGACCAAGCTACCCTAC 3 17 0 AGGATGGCAA 0.993072 -155 ******* *** Masking position 4 Map Score: 2.94383 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 99 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 AGGAACAGGGCTGCAGTCAATATATCCAAG 1 70 1 CTGCAGTCAA 0.974372 -231 AACCTGGACCCTGTGGTCAAGGTTTCCGCT 1 157 0 CTGTGGTCAA 0.955667 -144 CCAAGCTACCCTACGGTCCC 3 1 0 CTACGGTCCC 0.988144 -171 CACCGGAACGCTGGAGACCCGAGTTCAAAT 3 91 1 CTGGAGACCC 0.956302 -81 GTTCAAATCTCGGCGGTCCCATCAAATCGA 3 113 1 CGGCGGTCCC 0.994918 -59 ********** Masking position 6 Map Score: 1.94002 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 266 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 CAGCAAGGGATAAGATCGAGAGGGCCGGGG 1 209 1 TAAGATCGAG 0.903003 -92 CTTTAGTTTATAAAATAAAAATATATAAAG 2 23 0 TAAAATAAAA 0.817246 -36 TTTTATTTTATAAACTAAAGAGTAGAATGA 2 33 1 TAAACTAAAG 0.918371 -26 TCCGGACTTTTCAACTGGAACGGGGATGGT 3 58 1 TCAACTGGAA 0.893874 -114 GGCGGTCCCATCAAATCGAATCCAAGAACC 3 124 1 TCAAATCGAA 0.949228 -48 AGAAAAACATTAAAATAGAGGTTCTTGGAT 3 143 0 TAAAATAGAG 0.936101 -29 CACCTCATAATAAACTCTAGACTGAAAAAT 4 27 0 TAAACTCTAG 0.901925 -25 TCTATCACCTCAAATAAGTTTCAA 5 14 0 TCACCTCAAA 0.815439 -14 ********** Masking position 3 Map Score: 1.53775 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 196 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TTCTCGTGCCTGGAAAGGTCCTTGGAAGCGGA 1 131 1 TGGAAAGTCT 0.913879 -170 TCCTTGGAAGCGGAAACCTTGACCACAGGGTC 1 149 1 CGGAAACTGA 0.984264 -152 GCCTGACACTCGGAAAAATTGTTGAAGAGAAC 1 245 1 CGGAAAATGT 0.982974 -56 ACTGAATCATTCTACTCTTTAGT 2 46 0 CTGAATCTCT 0.878747 -13 TTGAAAAGTCCGGAAACTTCTTCAATGGCTGG 3 40 0 CGGAAACTTT 0.982964 -132 TGGTCAGCACCGGAACGCTGGAGACCCGAGTT 3 84 1 CGGAACGTGA 0.909577 -88 AAACTCTAGACTGAAAAATAGTGGTTTATTAG 4 14 0 CTGAAAATGT 0.957569 -38 ATATTGAAACTTATTTGAGGTGATA 5 4 1 TTGAAACTTT 0.83771 -24 ******* * ** Masking position 5 Map Score: 3.43551 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 146 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 ********** No masking Map Score: -7.36532e-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 9 ********** No masking Map Score: -7.36532e-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 10 ********** No masking Map Score: -7.36532e-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