AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i221_Ribosomal_Operon_8_mthe_reg_300.orf -o221_mthe_300.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 GAAAGGCCCACAAGGAACAGGGCTGCAGTCAATAT 1 58 1 CAAGGCGGTG 0.989379 -243 TCCAAGATAAACAGGCACTCCGATGAGGATGAAAC 1 94 1 ACAGGCCGTG 0.995013 -207 TCGTGCCTGGAAAGGTCCTTGGAAGCGGAAACCTT 1 134 1 AAAGGCGGAG 0.995447 -167 AACCTTGACCACAGGGTCCAGGTTGTTGCCCTGTC 1 163 1 ACAGGCGGTG 0.999037 -138 GATAAGATCGAGAGGGCCGGGGGAGAGTGCCTGAC 1 217 1 AGAGGCGGAG 0.997052 -84 GGACTTTTCAACTGGAACGGGGATGGTCAGCACCG 3 61 1 ACTGGCGGTG 0.995381 -111 GATGGTCAGCACCGGAACGCTGGAGACCCGAGTTC 3 82 1 ACCGGCTGAG 0.962719 -90 ACATTAAAATAGAGGTTCTTGGATTCGATTTGATG 3 132 0 AGAGGCGGTT 0.983761 -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 GACTCGAAAGGCCCACAAGGAACAGGGCTG 1 53 1 GCCCACAAGG 0.849542 -248 CGGAAACCTTGACCACAGGGTCCAGGTTGT 1 159 1 GACCACAGGG 0.991918 -142 TGTCTGTGAAAATGACAGGGCAACAACCTG 1 181 0 AATGACAGGG 0.940201 -120 CATTTTCACAGACAGCAAGGGATAAGATCG 1 197 1 GACAGCAAGG 0.933902 -104 ATAAGATCGAGAGGGCCGGGGGAGAGTGCC 1 218 1 GAGGGCCGGG 0.988225 -83 TTATGTTCTTAATGGCCGGGTTCTCTTCAA 1 266 0 AATGGCCGGG 0.978933 -35 GGGACCGTAGGGTAGCTTGGTC 3 3 1 GACCGTAGGG 0.973482 -169 AAACTTCTTCAATGGCTGGGAGGATGGACC 3 29 0 AATGGCTGGG 0.922047 -143 GATTTGATGGGACCGCCGAGATTTGAACTC 3 111 0 GACCGCCGAG 0.97295 -61 ********** Masking position 10 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 GAGGATGAAACAGTTCTCGTGCCTGGAAAGGTCCTT 1 118 1 CGTCGTGCGG 0.992537 -183 CCCTTGCTGTCTGTGAAAATGACAGGGCAACAACCT 1 182 0 CGTAATGCGG 0.997757 -119 CTTCAACAATTTTTCCGAGTGTCAGGCACTCTCCCC 1 236 0 TTTAGTGCGG 0.987549 -65 ATTATCTTTATGTTCTTAATGGCCGGGTTCTCTTCA 1 267 0 TTTAATGCGG 0.989657 -34 AGTCCGGAAACTTCTTCAATGGCTGGGAGGATGGAC 3 30 0 CTCAATGCGG 0.990434 -142 ATCCCCGTTCCAGTTGAAAAGTCCGGAAACTTCTTC 3 49 0 CGTAAAGCGG 0.990975 -123 * ** **** * ** Masking position 11 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 0.992378 -294 GCAATCTGGAAGGACGTTGCAAGGAGACTCGA 1 28 1 AGGACGTCAA 0.969135 -273 CACTCCGATGAGGATGAAACAGTTCTCGTGCC 1 109 1 AGGATGACAG 0.99532 -192 ACTAAAGAGTAGAATGATTCAGT 2 46 1 AGAATGACAG 0.97605 -13 AATGGCTGGGAGGATGGACCAAGCTACCCTAC 3 17 0 AGGATGGCAA 0.993197 -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 CTTGGATATATTGACTGCAGCCCTGTTCCT 1 70 0 TTGACTGCAG 0.976404 -231 AGCGGAAACCTTGACCACAGGGTCCAGGTT 1 157 1 TTGACCACAG 0.959118 -144 GGGACCGTAGGGTAGCTTGG 3 1 1 GGGACCGTAG 0.989097 -171 ATTTGAACTCGGGTCTCCAGCGTTCCGGTG 3 91 0 GGGTCTCCAG 0.959707 -81 TCGATTTGATGGGACCGCCGAGATTTGAAC 3 113 0 GGGACCGCCG 0.995329 -59 ********** Masking position 5 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 TCCGCTTCCAAGGACCTTTCCAGGCACGAGAA 1 131 0 AGACTTTCCA 0.908706 -170 GACCCTGTGGTCAAGGTTTCCGCTTCCAAGGA 1 149 0 TCAGTTTCCG 0.98323 -152 GTTCTCTTCAACAATTTTTCCGAGTGTCAGGC 1 245 0 ACATTTTCCG 0.981857 -56 ACTAAAGAGTAGAATGATTCAGT 2 46 1 AGAGATTCAG 0.87168 -13 CCAGCCATTGAAGAAGTTTCCGGACTTTTCAA 3 40 1 AAAGTTTCCG 0.981846 -132 AACTCGGGTCTCCAGCGTTCCGGTGCTGACCA 3 84 0 TCACGTTCCG 0.904112 -88 CTAATAAACCACTATTTTTCAGTCTAGAGTTT 4 14 1 ACATTTTCAG 0.95486 -38 TATCACCTCAAATAAGTTTCAATAT 5 4 0 AAAGTTTCAA 0.828718 -24 ** * ******* Masking position 4 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 7 CCCCGGCCCTCTCGATCTTATCCCTTGCTG 1 209 0 CTCGATCTTA 0.909111 -92 CTTTATATATTTTTATTTTATAAACTAAAG 2 23 1 TTTTATTTTA 0.827725 -36 TCATTCTACTCTTTAGTTTATAAAATAAAA 2 33 0 CTTTAGTTTA 0.923594 -26 ACCATCCCCGTTCCAGTTGAAAAGTCCGGA 3 58 0 TTCCAGTTGA 0.900495 -114 GGTTCTTGGATTCGATTTGATGGGACCGCC 3 124 0 TTCGATTTGA 0.952578 -48 ATCCAAGAACCTCTATTTTAATGTTTTTCT 3 143 1 CTCTATTTTA 0.940263 -29 ATTTTTCAGTCTAGAGTTTATTATGAGGTG 4 27 1 CTAGAGTTTA 0.908095 -25 TTGAAACTTATTTGAGGTGATAGA 5 14 1 TTTGAGGTGA 0.826001 -14 ********** Masking position 5 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 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