AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i036_mgen_mpneu_300.orf -o036_mgen_mpneu_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -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 = 0.36 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMG04524 17 Mycoplasma #2 RMP00406 300 Mycoplasma_pneumoniae #3 RMP00408 55 Mycoplasma_pneumoniae #4 RMP00409 157 Mycoplasma_pneumoniae #5 RMP00412 30 Mycoplasma_pneumoniae #6 RMP00414 37 Mycoplasma_pneumoniae Motif number 1 ttgctttaactaacctgcttttatctaacta 2 57 0 taactgcttt 0.81224 -244 tttgtcatgccatcgtggtttaaaatgtaca 2 132 1 catctggttt 0.881438 -169 cccactggtgcaactagcttaatctcttggc 2 170 0 caacagctta 0.892716 -131 ataagtaagaaaaactgctttagtgcccact 2 195 0 aaaatgcttt 0.96594 -106 ttttaggtaaaaactagcttttaaagtgcca 2 236 1 aaacagcttt 0.940951 -65 taacgcggtttttgctctcta 2 290 0 taaccggttt 0.850052 -11 ctcaaacgctaaaagtgctaacgatttgttt 3 13 1 aaaatgctaa 0.845547 -43 agagggcagttaaactgctctttttttatgt 4 36 1 taaatgctct 0.876028 -122 tttgacctgtaataatggtttatagacgtct 4 71 1 aatatggttt 0.904693 -87 aaatggtttaaaaagtgcttaaagacgtcta 4 93 0 aaaatgctta 0.977155 -65 gactaattgaaaaaatggtttaaaaagtgct 4 105 0 aaaatggttt 0.965631 -53 aaaaacctgcttacttagtttta 6 25 0 aaactgctta 0.828681 -13 **** ****** Masking position 2 Map Score: 15.3535 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 316 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 agtaaatctattcctgttttaatccgcttatc 2 21 0 tcctttttaa 0.867362 -280 aaacgttttttttttttttttgaaagaaattg 2 89 0 tttttttttg 0.949771 -212 ttaatctcttggcttaattttgtacattttaa 2 151 0 gcttattttg 0.950493 -150 tacttatcaatacttatttttaggtaaaaact 2 219 1 tcttttttta 0.987977 -82 gttaaatttttgctttattttggcactttaaa 2 255 0 tcttattttg 0.934668 -46 aagtgctaacgatttgtttataatatttagca 3 25 1 gttttttata 0.83734 -31 cagtttaactgccctctttttattgatctact 4 21 0 gcctttttta 0.985728 -137 cagttaaactgctctttttttatgtcttattt 4 42 1 gtctttttta 0.962085 -116 ttttcaattagtcttatttttaaaatttaaaa 4 123 1 gcttttttta 0.991013 -35 tttaagtttttatttttaaattttaaaa 4 140 0 ttttttttta 0.967938 -18 aaaacctgcttacttagttttactctttactt 6 15 0 tcttgtttta 0.950492 -23 * *** ****** Masking position 5 Map Score: 14.4726 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 222 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 gataagcggattaaaacaggaatagatttac 2 21 1 ttaaaacaga 0.860778 -280 aatagttagataaaagcaggttagttaaagc 2 55 1 taaaagcagt 0.937196 -246 agcaggttagttaaagcaatcaatttctttc 2 69 1 ttaaagcatc 0.912573 -232 tttgtacattttaaaccacgatggcatgaca 2 134 0 ttaaaccaga 0.975589 -167 atgtacaaaattaagccaagagattaagcta 2 156 1 ttaagccaga 0.853522 -145 aagccaagagattaagctagttgcaccagtg 2 168 1 attaagctgt 0.805363 -133 ccagtgggcactaaagcagtttttcttactt 2 193 1 ctaaagcatt 0.891254 -108 tttggcactttaaaagctagtttttacctaa 2 238 0 taaaagctgt 0.813631 -63 aagtgccaaaataaagcaaaaatttaacctt 2 259 1 ataaagcaaa 0.765257 -42 aaagcaaaaatttaacctttagagagcaaaa 2 271 1 tttaacctta 0.723927 -30 aaagacgtctataaaccattattacaggtca 4 73 0 ataaaccata 0.908673 -85 tatagacgtctttaagcactttttaaaccat 4 91 1 tttaagcatt 0.942623 -67 taagcactttttaaaccattttttcaattag 4 103 1 ttaaaccatt 0.961388 -55 agtaaaactaagtaagcaggttttt 6 23 1 agtaagcagt 0.708228 -15 ******** ** Masking position 4 Map Score: 9.12169 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 570 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 atgacaaacttacaatttcaaacgttttttttt 2 107 0 taatttcaac 0.93032 -194 catcgtggtttaaaatgtacaaaattaagccaa 2 142 1 taatgtaaaa 0.97446 -159 aactagcttttaaagtgccaaaataaagcaaaa 2 247 1 taatgccaaa 0.92444 -54 atttaacctttagagagcaaaaaccgcgtta 2 280 1 taaagcaaaa 0.930881 -21 gtttatgtgctaaatattataaacaaatcgtta 3 31 0 taaattaaaa 0.937226 -25 tttttatttttaaattttaaaaataagactaat 4 129 0 taatttaaaa 0.960086 -29 ctaattagtttatattttactact 5 2 0 taatttatac 0.808622 -29 attaaagtaaagagtaaaactaagtaagca 6 8 1 taaagtaaac 0.958868 -30 ** * **** *** Masking position 4 Map Score: 4.14752 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 21 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 ********** No masking Map Score: 1.34536e-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 6 ********** No masking Map Score: 1.34536e-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 7 ********** No masking Map Score: 1.34536e-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