AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_mpneu_reg_300.orf -o020_mpneu_300.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMP00447 21 Mycoplasma_pneumoniae Input sequences: #1 RMP00443 255 Mycoplasma_pneumoniae #2 RMP00444 166 Mycoplasma_pneumoniae #3 RMP00445 67 Mycoplasma_pneumoniae #4 RMP00446 20 Mycoplasma_pneumoniae #5 RMP00448 300 Mycoplasma_pneumoniae Motif number 1 ctcttaaagattggaattatcctggtcttagcttt 1 47 1 ttgattatgg 0.988655 -209 ttgggcctgtttggaattatttttggtagttataa 1 83 1 ttgattattg 0.987723 -173 gttagcgtccttggacttatggtttaaaaaataaa 1 174 0 ttgcttattt 0.937777 -82 ccgcacttaactaaacttagtttggcgtgaaaata 3 18 1 ctacttatgg 0.920818 -50 aatcaatgtcttaagattaatattttcacgccaaa 3 38 0 ttaattattt 0.897154 -30 tcaagccatttgaaataagtttggggtttgttag 5 10 1 ttaataatgg 0.93825 -291 acctagtttttttaactaaaagttgagaaggctag 5 54 1 ttactaattg 0.938261 -247 caccatttatttcatattaagatggaagacaagaa 5 93 1 ttaattatgg 0.982037 -208 ttagagaaatttcgccttatttttggcagcatttg 5 185 0 ttgcttattg 0.988657 -116 tggttttttatttgcattacttttgctttaaatct 5 253 1 ttgattattg 0.987726 -48 ** * **** *** Masking position 7 Map Score: 11.4842 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 52 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 gtttcctttgactggctcttaaagattggaa 1 32 1 actggcttta 0.940556 -224 cccctaagcgactgtcgtttagaagcttata 1 113 0 actgtcgtta 0.940556 -143 cactaccaccactgtttattttttaaaccat 1 160 1 actgtttttt 0.979563 -96 aacgcttttaacagtttttaagataataaac 2 13 1 acagttttaa 0.799451 -154 tttctgtttcactgtttattatcttaaaaac 2 26 0 actgttttta 0.975807 -141 caaacaattcactgtttaaaaaaattggcgt 2 129 0 actgtttaaa 0.864853 -38 tgcaaccgccacagttgcatttactgcagtt 5 156 0 acagttgatt 0.747913 -145 cagtcttacgactggctttttatctaaaacg 5 224 0 actggctttt 0.949501 -77 cagtcgtaagactggttttttatttgcatta 5 241 1 actggttttt 0.967763 -60 tatttgcattacttttgctttaaatctaaaa 5 261 1 acttttgttt 0.702858 -40 gatataaaaactgttttaattttagattta 5 281 0 actgtttaat 0.883782 -20 ******* *** Masking position 1 Map Score: 11.2757 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 235 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 tcaaaggaaacccgctttttcagtcccact 1 13 0 cccgcttttt 0.924323 -243 tatcctggtcttagcttttttgggcctgtt 1 64 1 ttagcttttt 0.791313 -192 actaccaccactgtttattttttaaaccat 1 161 1 ctgtttattt 0.800464 -95 gctgccattgccgtcctttttctgggtagg 1 221 0 ccgtcctttt 0.908224 -35 gacattacgccaatttttttaaacagtgaa 2 123 1 caattttttt 0.772891 -44 tcaagccatttgaaataagtt 5 2 1 caagccattt 0.814648 -299 ataattgcacctagtttttttaactaaaag 5 46 1 ctagtttttt 0.961981 -255 atggtgttccctagccttctcaacttttag 5 69 0 ctagccttct 0.850214 -232 ctagggaacaccatttatttcatattaaga 5 85 1 ccatttattt 0.753342 -216 agtcttacgactggctttttatctaaaacg 5 224 0 ctggcttttt 0.981181 -77 agtcgtaagactggttttttatttgcatta 5 242 1 ctggtttttt 0.964805 -59 ********** Masking position 8 Map Score: 6.79082 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 296 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 atctaactccttgttagcgtccttggactt 1 191 0 ttgttagcgt 0.981344 -65 ttcagtattgttaccgctgccattgcc 1 239 0 ttgttaccgc 0.957977 -17 ctccaagcgcttgatcgagctattaagcga 2 57 1 ttgatcgagc 0.933387 -110 aaacagtgaattgtttgagtttgtactgga 2 143 1 ttgtttgagt 0.961711 -24 ttgttccagtacaaactcaa 2 157 0 ttgttccagt 0.972832 -10 agtttggggtttgttagaataattgcacct 5 28 1 ttgttagaat 0.907559 -273 ********** Masking position 5 Map Score: 2.82865 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 62 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 tagtgttcaacggttccactaccaccactgttt 1 144 1 cggttccatc 0.993881 -112 gtattgttaccgctgccattgccgtcctttttc 1 229 0 cgctgccatc 0.968789 -27 ctcgatcaagcgcttggagtttctgtttcactg 2 43 0 cgcttggatc 0.973849 -124 agaaatgctgtggttgcaaaaccgaaacagcta 5 124 1 tggttgcaac 0.962633 -177 gcaaccgccacagttgcatttactgcagttagc 5 153 0 cagttgcatc 0.979622 -148 gcaactgtggcggttgcaaatgctgccaaaaat 5 169 1 cggttgcaac 0.994031 -132 ******** * * Masking position 8 Map Score: 2.54405 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 43 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 taattccaaacaggcccaaaaaagctaaga 1 72 0 caggcccaaa 0.913729 -184 aagcttataactaccaaaaataattccaaa 1 92 0 ctaccaaaaa 0.957155 -164 ccgttgaacactacccctaagcgactgtcg 1 127 0 ctacccctaa 0.969322 -129 gagttagatcctacccagaaaaaggacggc 1 212 1 ctacccagaa 0.967515 -44 ttattctaacaaaccccaaacttatttcaa 5 20 0 aaaccccaaa 0.896047 -281 gttgcaaatgctgccaaaaataaggcgaaa 5 181 1 ctgccaaaaa 0.948772 -120 ********** Masking position 9 Map Score: 0.757045 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 136 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 gaattatcctggtcttagcttttttgggcc 1 60 1 ggtcttagct 0.965081 -196 acgctaacaaggagttagatcctacccaga 1 201 1 ggagttagat 0.940163 -55 ataaataccgcacttaactaaacttagtt 3 10 1 gcacttaact 0.962094 -58 tagaataattgcacctagtttttttaacta 5 42 1 gcacctagtt 0.937569 -259 tgcatttactgcagttagctgtttcggttt 5 142 0 gcagttagct 0.989122 -159 ********** Masking position 6 Map Score: 0.419904 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 67 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ********** No masking Map Score: -1.56076e-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: -1.56076e-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 10 ********** No masking Map Score: -1.56076e-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