AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_mpneu_reg_100.orf -o020_mpneu_100.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 RMP00444 166 Mycoplasma_pneumoniae #2 RMP00445 67 Mycoplasma_pneumoniae #3 RMP00446 20 Mycoplasma_pneumoniae #4 RMP00448 300 Mycoplasma_pneumoniae Motif number 1 agctcgatcaagcgcttggagtttctgtttcactgtttat 1 38 0 acttgatttt 0.897687 -129 ttaaacagtgaattgtttgagtttgtactggaacaa 1 141 1 attttatttg 0.982365 -26 accgcacttaactaaacttagtttggcgtgaaaatattaa 2 17 1 atactatttg 0.771182 -51 atcgtaatcaatgtcttaagattaatattttcacgccaa 2 39 0 atcttatttt 0.962402 -29 tcaagccatttgaaataagtttggggtttgtta 4 4 1 actttatatg 0.894911 -297 aattgcacctagtttttttaactaaaagttgagaaggcta 4 48 1 attttatatt 0.959528 -253 agggaacaccatttatttcatattaagatggaagacaaga 4 87 1 attttatttg 0.982364 -214 ccacagttgcatttactgcagttagctgtttcggttttgc 4 139 0 atctgatatt 0.796553 -162 ataaggcgaaatttctctaaatttcgttttagataaaaag 4 200 1 attctatttt 0.95809 -101 cagtcgtaagactggttttttatttgcattacttttgctt 4 241 1 attttttttt 0.883289 -60 gatataaaaactgttttaattttagatttaaagcaaaag 4 272 0 attttatttt 0.983488 -29 * * *** * ** ** Masking position 1 Map Score: 7.31887 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 137 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 ttaacagtttttaagataataaacagtgaa 1 20 1 ttaagataat 0.696005 -147 caattcactgtttaaaaaaattggcgtaat 1 126 0 tttaaaaaaa 0.58311 -41 ccaaactaagtttagttaagtgcggtattt 2 13 0 tttagttaag 0.841254 -55 aatcaatgtcttaagattaatattttcacg 2 43 0 ttaagattaa 0.900955 -25 aattatttgttagtttaatc 3 3 0 gttagtttaa 0.872854 -18 tttggggtttgttagaataattgcacctag 4 30 1 gttagaataa 0.829566 -271 cttctcaacttttagttaaaaaaactaggt 4 54 0 tttagttaaa 0.826097 -247 taaaacgaaatttagagaaatttcgcctta 4 201 0 tttagagaaa 0.931738 -100 taaatttcgttttagataaaaagccagtcg 4 217 1 tttagataaa 0.939999 -84 ctgttttaattttagatttaaagcaaaagt 4 271 0 tttagattta 0.834141 -30 ********** Masking position 4 Map Score: 8.21444 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 187 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 agcgcttggagtttctgtttcactgtttat 1 38 0 gtttctgttt 0.983624 -129 acagtgaattgtttgagtttgtactggaac 1 145 1 gtttgagttt 0.976323 -22 tttgaaataagtttggggtttgttagaata 4 19 1 gtttggggtt 0.986632 -282 gcagttagctgtttcggttttgcaaccaca 4 132 0 gtttcggttt 0.995827 -169 atttctctaaatttcgttttagataaaaag 4 210 1 atttcgtttt 0.897568 -91 ********** Masking position 4 Map Score: 4.26775 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 30 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 attgcacctagtttttttaactaaaagttga 4 49 1 gttttttaac 0.966187 -252 gtgttccctagccttctcaacttttagttaa 4 65 0 gcttctcaac 0.942694 -236 tagctgtttcggttttgcaaccacagcattt 4 126 0 ggtttgcaac 0.984743 -175 atttttggcagcatttgcaaccgccacagtt 4 171 0 gctttgcaac 0.977936 -130 tcttacgactggctttttatctaaaacgaaa 4 221 0 ggtttttatc 0.980208 -80 tcgtaagactggttttttatttgcattactt 4 244 1 ggtttttatt 0.865299 -57 aattaaaacagtttttatatc 4 290 1 gttttatatc 0.869654 -11 ** ******** Masking position 9 Map Score: 3.3055 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 128 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 ********** No masking Map Score: -8.21797e-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 6 aaaaactgttaaaagcgtttc 1 1 0 aaaagctttc 0.908151 -166 tcactgtttaaaaaaattggcgtaatgtcgt 1 121 0 aaaaaatggc 0.932343 -46 ttttagttaaaaaaactaggtgcaattattc 4 44 0 aaaaacaggt 0.925674 -257 aagatggaagacaagaaatgctgtggttgca 4 111 1 acaagaatgc 0.86123 -190 aaatgctgccaaaaataaggcgaaatttctc 4 186 1 aaaaataggc 0.974154 -115 gttttagataaaaagccagtcgtaagactgg 4 225 1 aaaagcagtc 0.985744 -76 aatgcaaataaaaaaccagtcttacgactgg 4 240 0 aaaaacagtc 0.977577 -61 gatttaaagcaaaagtaatgcaaataaaaaa 4 256 0 aaaagtatgc 0.958958 -45 ****** **** Masking position 4 Map Score: 5.87036 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 118 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 ********** No masking Map Score: -8.21797e-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: -8.21797e-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: -8.21797e-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