AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i301_mgen_mpneu_300.orf -o301_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 Purged sequences: RMP00371 18 Mycoplasma_pneumoniae Input sequences: #1 RMG00022 300 Mycoplasma #2 RMG01110 46 Mycoplasma #3 RMG00025 65 Mycoplasma #4 RMG02159 188 Mycoplasma #5 RMG01114 41 Mycoplasma #6 RMG00035 29 Mycoplasma #7 RMG02168 26 Mycoplasma #8 RMG00037 202 Mycoplasma #9 RMG04456 38 Mycoplasma #10 RMG03425 36 Mycoplasma #11 RMG04443 58 Mycoplasma #12 RMP00126 20 Mycoplasma_pneumoniae #13 RMP00127 32 Mycoplasma_pneumoniae #14 RMP00368 300 Mycoplasma_pneumoniae Motif number 1 TATTTTGGTTAAATTAAAATTGTTATAATAATTAGTTA 1 229 0 AAATAAATAA 0.93911 -72 GCTGTTTTGATTATAAAAACTGTTAAAATTCGAGGGGT 1 266 0 TTATAAATAA 0.745923 -35 TGAAGTAATTAATCTCTTTAAAATCTTTCAAGA 2 24 0 TAATAATTAA 0.979869 -23 ATAAATTTAATAGTGTTGAAAGACaAACATT 3 4 1 AATTAATTAA 0.841438 -62 CTCAAAAAACTAATACATCAAACTTCAACCGTTTACTT 4 11 1 TAATCATTAA 0.924007 -178 AATCTATTTGAAATAATTCTTCATAAAACCTTTGTAGT 4 63 0 AAATATTTAA 0.955975 -126 TTCTGCTAAATCAATGGTTTTGTAATCATCAAAAA 4 164 0 AAATAATTAA 0.984131 -25 AGCAAGAATTATAATTAACACTCTAAGGATGCAAGT 5 9 1 TTATATTTAA 0.809127 -33 AAATCAATAAAATTCTAATACTACTTTT 6 12 0 AAATAATTAA 0.984131 -18 AAATTAATCTATTTTCAAAATGAGTTTT 8 1 1 AAATAATTAA 0.984132 -202 CATTAATTTTTAATTAATAAATGTTGAAAAAACTCATT 8 29 0 TAATAATTAA 0.979877 -174 TATTAATTAAAAATTAATGCTTTTTAAAGTTGAATCTT 8 48 1 AAATAATTAA 0.984132 -155 AAGTATTGAAAAATGAATTAAGATTCAACTTTAAAAAG 8 67 0 AAATAATTAA 0.984132 -136 GATAATATACTTATTTATCTAATATTCCAACA 9 5 1 ATATCTTTAA 0.574159 -34 AGCTAATAATTAAAAGTCTAATTTTTATTGT 10 16 0 TAATATTTAA 0.944236 -21 TATATATTAATAATTAAACATTTTAAAAGTCTTATAAA 11 28 0 TAATAAATAA 0.923636 -31 **** *** * ** Masking position 14 Map Score: 24.9249 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 82 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 AATTAGCTGTTTTGATTATAAAAACTGTTAAA 1 277 0 TTTGATTTAA 0.851407 -24 GACaAACATTATTAATTTTTGATCAGCTAAAT 3 32 1 ATTAATTTTA 0.932176 -34 ACTTCAACCGTTTACTTTTTTATGAACAAGCA 4 32 1 TTTACTTTTA 0.956334 -157 ATCTATTTGAAATAATTCTTCATAAAACCTTT 4 68 0 AATAATTTTA 0.884633 -121 AAAAGCGCAATTTGATTCTTATCTTTAATGGG 4 124 0 TTTGATTTTT 0.754359 -65 GAGTGTTAATTATAATTCTTGCT 5 2 0 TATAATTTTC 0.72169 -40 TAGATATGCTTGTTAACTTTAAATTG 7 5 1 TATGCTTTTA 0.871644 -22 TTTAAAAAGCATTAATTTTTAATTAATAAATG 8 44 0 ATTAATTTTA 0.932166 -159 TTCATTTTTCAATACTTTTTTAGGCTTCCTAT 8 88 1 AATACTTTTA 0.840625 -115 TTTCTTAACTTTTACTTTTAGAAAAGCGTATT 8 134 0 TTTACTTTAA 0.876423 -69 AAAACGTTTTTATAATTTTAGAGATAGTT 8 184 1 TATAATTTAA 0.851913 -19 GATAATATACTTATTTATCTAATATTC 9 6 1 TATACTTTTA 0.924403 -33 AAAGTCTAATTTTTATTGTTAATT 10 3 0 TTTTATTTTA 0.772246 -34 AAATTAGACTTTTAATTATTAGCT 10 23 1 TTTAATTTTG 0.822943 -14 AATTCGATTATTTAATTTTATAAGACTTTTAA 11 12 1 TTTAATTTAA 0.909965 -47 TTTTAAAATGTTTAATTATTAATATATAGCT 11 38 1 TTTAATTTTA 0.969569 -21 aaaattgcgaattgattgttctttctctaact 14 169 0 attgattttt 0.569834 -132 ******* ** * Masking position 6 Map Score: 15.8987 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 283 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 CCTGAGTGCAAATCAGGTGCTCTATCAGTTGAGC 1 83 1 AATAGTGTTA 0.861818 -218 CCTCGAATTTTAACAGTTTTTATAATCAAAACAG 1 269 1 TAAAGTTTTA 0.637217 -32 GAAAGATTTTAAAGAGATTAATTACTTCA 2 28 1 AAAAGTTATA 0.655098 -19 GAATTATTTCAAATAGATTATTTAAGAAGATTTG 4 82 1 AAAAGTTTTA 0.946936 -107 GTAATCATCAAAAACAGTTTTAAAAAGCGCAATT 4 144 0 AAACATTTAA 0.764634 -45 GATGATTACAAAACCATTGATTTAGCAGAA 4 169 1 AAACATGTTA 0.879806 -20 CTATTTTCAAAATGAGTTTTTTCAACATTTATTA 8 19 1 AATAGTTTCA 0.699392 -184 GTTGAATCTTAATTCATTTTTCAATACTTTTTTA 8 76 1 AATCATTTAA 0.711555 -127 TAATTAAATTAATACGCTTTTCTAAAAGTAAAAG 8 124 1 AATCGTTTTA 0.971514 -79 TATTCAAACAAAAACGTTTTTATAATTTTAGAGA 8 174 1 AAACGTTTTA 0.978215 -29 GATAATATACTTATTTATCTAATATTC 9 4 1 AATTATTTTA 0.542099 -35 TAATTCGATTATTTAATTTTATAAG 11 2 1 AATCGTTTTA 0.971505 -57 ttgatgtgttaaaccacttcgctaaccaactcca 14 246 1 aaacattgta 0.715002 -55 cataaaccgcaaaccgttgatctaaca 14 284 1 aaacgtgtta 0.953853 -17 *** ** ** * ** Masking position 2 Map Score: 7.89478 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 170 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 GATGAAGGGTCTCAAACCCTCAACCTCCTGA 1 57 1 CTAAACCCTC 0.893168 -244 AGTAAATGGACTTGAACCATCGACCTCACCC 1 138 1 CTGAACCATC 0.980196 -163 CAGGGGTGTGCTCTAACCAACTGAGCTATAC 1 173 1 CTTAACCAAC 0.983608 -128 ttgacgaaaacttaaacgaacaaagtttgct 14 25 1 ctaaacgaac 0.942954 -276 gcatgagttgcttgagcaaactttgttcgtt 14 39 0 ctgagcaaac 0.908513 -262 taacattaccctagaaccaacaagggaaaca 14 80 1 ctgaaccaac 0.992658 -221 atggtgtggtcaaaagccaaccccatgttga 14 219 1 caaagccaac 0.909977 -82 taaaccacttcgctaaccaactccaagttca 14 255 1 cgtaaccaac 0.948623 -46 ** ******** Masking position 5 Map Score: 5.562 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 34 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 GGGTCTCAAACCCTCAACCTCCTGAGTGCA 1 63 1 CCCTCAACCT 0.853601 -238 CAGTTGAGCTACATCCCCATTATTGGTGGA 1 108 1 ACATCCCCAT 0.97226 -193 TGAACCATCGACCTCACCCTTATCAGGGGT 1 150 1 ACCTCACCCT 0.987037 -151 AAAAACTAATACATCAAACTTCAACCGTTT 4 15 1 ACATCAAACT 0.747857 -174 AGATTTGAAAACATTCCCATTAAAGATAAG 4 109 1 ACATTCCCAT 0.889092 -80 TTTGATGATTACAAAACCATTGATTTAGCA 4 166 1 ACAAAACCAT 0.74613 -23 aaaacccgtaacattaccctagaaccaaca 14 72 1 acattaccct 0.95478 -229 ttggcttttgaccacaccatatctaccata 14 209 0 accacaccat 0.949212 -92 gtggtttaacacatcaacatggggttggct 14 233 0 acatcaacat 0.959183 -68 ********** Masking position 10 Map Score: 5.50352 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 63 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 GTGCTCTATCAGTTGAGCTACATCCCCATT 1 99 1 AGTTGAGCTA 0.949696 -202 TGCTCTAACCAACTGAGCTATACTTCCAAG 1 181 1 AACTGAGCTA 0.958779 -120 TGAAGTAATTAATCTCTTTAAAATCT 2 31 0 AATTAATCTC 0.779318 -16 TGTTTTATTTAGCTGATCAAAAATTAATAA 3 40 0 AGCTGATCAA 0.878271 -26 AAATCTTCTTAAATAATCTATTTGAAATAA 4 85 0 AAATAATCTA 0.801632 -104 AAATTAATCTATTTTCAAAAT 8 2 1 AATTAATCTA 0.930049 -201 ttctttctctaactgatctaattcgccaaa 14 153 0 aactgatcta 0.976233 -148 aaccgcaaaccgttgatctaaca 14 288 1 cgttgatcta 0.898531 -13 ********** Masking position 6 Map Score: 2.28087 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 57 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TCTAACTTACCTTTGCATAAATA 1 2 0 CTTTATAAAT 0.889341 -299 TCATCTCCACCATTAAAGAATTCCAACGTCTA 1 30 0 CATTAGAATT 0.739534 -271 TCCTAAGGGTATTTAACTAATTATTATAACAA 1 216 1 ATTTCTAATT 0.561062 -85 TCTTTAAAATCTTTCAAGAACTTGGTTTTACA 2 11 0 CTTTAGAACT 0.929936 -36 TTGCTTTGTTTTATTTAGCTGATCA 3 51 0 CTTTTTTATT 0.780156 -15 TCAAATTGCGCTTTTTAAAACTGTTTTTGATG 4 141 1 CTTTAAAACT 0.769934 -48 GTTTTTTCAACATTTATTAATTAAAAATTAAT 8 34 1 CATTTTAATT 0.779508 -169 GCTTCCTATTCTTTAATTAAATTAATACGCTT 8 111 1 CTTTTTAAAT 0.83832 -92 AATAAAAGTACTTTTCTTAACTTTTACTTTTA 8 146 0 CTTTTTAACT 0.942023 -57 AAACAAAAACGTTTTTATAATTTTAGAGATAG 8 179 1 GTTTATAATT 0.729823 -24 AAAAATTAGACTTTTAATTATTAGCT 10 21 1 CTTTATTATT 0.838586 -16 aacgtagtttctttggcgaattagatcagtta 14 142 1 ctttcgaatt 0.921375 -159 attgattgttctttctctaactgatctaattc 14 159 0 ctttctaact 0.951313 -142 **** ****** Masking position 10 Map Score: 6.57991 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 217 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 TGGAATTCTTTAATGGTGGAGATGAAGGGT 1 37 1 TAATGGTGGA 0.976103 -264 ACATCCCCATTATTGGTGGAAGTAAATGGA 1 118 1 TATTGGTGGA 0.966109 -183 ATAAAAACGTTTTTGTTTGAATAAAAGTAC 8 167 0 TTTTGTTTGA 0.820238 -36 GGATTATGTTGGAATATTAGATA 9 26 0 TTATGTTGGA 0.962931 -13 ttttttcactttatggtagatatggtgtgg 14 198 1 ttatggtaga 0.936433 -103 ********** Masking position 4 Map Score: 1.09145 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 27 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 CCCCTGATAAGGGTGAGGTCGATGGTTCAA 1 149 0 GGGTGAGGTC 0.992364 -152 CCCTTATCAGGGGTGTGCTCTAACCAACTG 1 166 1 GGGTGTGCTC 0.992004 -135 atggtagatatggtgtggtcaaaagccaac 14 210 1 tggtgtggtc 0.98824 -91 ********** Masking position 4 Map Score: 0.416134 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 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 10 ********** No masking Map Score: -2.34236e-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 11 ********** No masking Map Score: -2.34236e-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 12 ********** No masking Map Score: -2.34236e-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