AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mgen_mpneu_100.orf -o294_mgen_mpneu_100.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: RMP00673 25 Mycoplasma_pneumoniae Input sequences: #1 RMG02253 110 Mycoplasma #2 RMG00273 137 Mycoplasma #3 RMG02389 24 Mycoplasma #4 RMG03341 101 Mycoplasma #5 RMG04342 161 Mycoplasma #6 RMG01004 115 Mycoplasma #7 RMP00207 76 Mycoplasma_pneumoniae #8 RMP00208 300 Mycoplasma_pneumoniae #9 RMP00212 86 Mycoplasma_pneumoniae #10 RMP00274 121 Mycoplasma_pneumoniae #11 RMP00287 27 Mycoplasma_pneumoniae #12 RMP00288 42 Mycoplasma_pneumoniae #13 RMP00296 54 Mycoplasma_pneumoniae #14 RMP00624 300 Mycoplasma_pneumoniae #15 RMP00677 300 Mycoplasma_pneumoniae Motif number 1 AAAACCAAGGTTTTATGGCTTTTAGTTATTATCG 1 22 0 TTTTGCTTTA 0.98731 -89 AAAACCTTGGTTTTGTGGTTTTTAGCTTGTTTAT 1 42 1 TTTTGTTTTA 0.944981 -69 TATAAACTTCTTTTTTATCCCTTATAAGCTAGGG 4 34 1 TTTTTCCTTA 0.866075 -68 AAATGACAAATTTGTAAGCTGTTACAAACACTAC 5 45 0 TTTAGCTTTA 0.900118 -117 ATTTTTCACTTTTCATTGCTATTAATAAGACAAA 5 75 1 TTTTGCTTTA 0.98731 -87 GATAAATGATTTTCATCGCCTTTGTTTTGTCTTA 5 100 0 TTTTGCCTTG 0.968979 -62 TTAGCTCTATTTTCGTTGCCATTATTGCACTAAG 6 84 0 TTTTGCCTTA 0.989026 -32 gccaacgcctttaagttgctgttacattttgtgc 7 17 0 ttatgcttta 0.975818 -60 ggattttaacttaagttgcttttgttaagttcga 8 38 1 ttatgctttg 0.933268 -263 taatcacgctttattttgtcgttaacgtaggaaa 8 187 0 ttatgtctta 0.911654 -114 ataaatcggtttatattgccattaatt 13 4 0 ttatgcctta 0.979055 -51 ggaaaggaaatttgttcgttattacactagatcg 15 270 0 ttttgtttta 0.944981 -31 *** * *** *** Masking position 12 Map Score: 17.3108 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 65 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 2 TTACTGCATAATGTAAAATTACACAGC 1 94 1 ATTAAAATTA 0.896257 -17 CACTACTAATAATTTAAATTAAGCACTCATA 2 52 1 AATTAAATTA 0.949036 -86 CAGCTTGAAGTAAAATTAATCCTA 3 8 1 AATAAAATTA 0.964709 -17 TTAAAATTTAAAATTATTGTGGTTAT 4 6 1 ATTAAAATTA 0.896257 -96 TATTAGTTAAAAATAAAGTTACTTA 5 5 0 AATAAAGTTA 0.921597 -157 gtccgcaatttaataaaattacctttcgcca 7 47 0 tataaaatta 0.879609 -30 taacaaaagcaacttaagttaaaatccctta 8 34 0 aattaagtta 0.889246 -267 ctatttcacaagctaaaattacggcgctggt 8 94 0 agtaaaatta 0.878954 -207 cgattgtccgaatttaaattataaataatcc 9 46 1 aattaaatta 0.949036 -41 tacttaaattatatttaacct 11 17 0 tattaaatta 0.834576 -11 ** ******** Masking position 6 Map Score: 9.66153 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 3 TGCTTAATTTAAATTATTAGTAGTGAATCT 2 47 0 AAATTATTAG 0.862786 -91 TTAATTACCAAAATTATTAAAATAATTGTT 6 18 0 AAATTATTAA 0.967896 -98 AGTAAATAAGAAATTATTAATTACCAAAAT 6 34 0 AAATTATTAA 0.967896 -82 ACTAAGCTTAATATTACTAATAAGATAGTA 6 60 0 ATATTACTAA 0.645864 -56 gttcgagttgtaattattaagttctgaaac 8 66 1 taattattaa 0.940462 -235 gtccgaatttaaattataaataatccatgt 9 51 1 aaattataaa 0.809251 -36 ctttgtttgcaaattattaaagacagcttg 10 72 1 aaattattaa 0.967896 -50 gtttaaattgtaattcttaaaccaacgccc 12 13 0 taattcttaa 0.767354 -30 gacgttcgaggaattattaagaataattcc 14 174 1 gaattattaa 0.902697 -127 tcaattgaattaattactaacgattggttg 14 246 0 taattactaa 0.87174 -55 ********** Masking position 5 Map Score: 9.45814 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 68 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 TTTAGTTATTATCGAGTTTTATTGA 1 4 0 ATCGGTTTAT 0.94557 -107 AAACCTGATTTATTTTTATAGAA 2 2 1 AACCGTTTAT 0.981019 -136 TTGTGGTTATAAACTTCTTTTTTATCCCTTAT 4 27 1 AAACTTTTTT 0.604967 -75 CAAACACTACAAACTGTTTTATTAGTTAAAAA 5 23 0 AAACGTTTAT 0.936931 -139 tgaaactataatcacgctttattttgtcgtta 8 197 0 atcagtttat 0.884173 -104 attataaataatccatgtttttagctaatgta 9 63 1 atcctttttt 0.821641 -24 tgaagctggcatcgagctttgtttgcaaatta 10 56 1 atcggtttgt 0.802347 -66 atggcaatataaaccgatttatcacagataaa 13 16 1 aaacgtttat 0.936825 -39 acgaagttaaaacctgttttatctgtgataaa 13 33 0 aaccgtttat 0.981021 -22 attgtgttggatacagatttatacttttt 14 8 0 atacgtttat 0.918333 -293 aaatgtacctatcaggatttttagggaattgt 14 35 0 atcagttttt 0.799802 -266 cgaattgtgaaaccgtgtttttaccacaacca 14 220 1 aacctttttt 0.842209 -81 gaccatcacaaacgcgatttaggtgggcatca 15 138 0 aacggtttag 0.760511 -163 **** * ***** Masking position 1 Map Score: 10.3181 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 93 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 CTTATTAATAGCAATGAAAAGTGAAAAATG 5 74 0 GCAATGAAAA 0.982103 -88 CAAAACAAAGGCGATGAAAATCATTTATCA 5 105 1 GCGATGAAAA 0.978492 -57 TGCAATAATGGCAACGAAAATAGAGCTAAT 6 89 1 GCAACGAAAA 0.978492 -27 caatttttgtccactgaaaaaccaaacgaa 14 122 0 ccactgaaaa 0.959643 -179 caaaaattgcccaccgaaaaattaacacct 14 143 1 ccaccgaaaa 0.951723 -158 aaacgattcggcgatgaaaacgcagaacat 15 94 1 gcgatgaaaa 0.978492 -207 ********** Masking position 7 Map Score: 6.09227 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 12 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 GATAATAACTAAAAGCCATAAAACCTTGGTTTTGTGG 1 23 1 AAAATAACTT 0.710359 -88 TAACTGTTTCTATAAAAATAAATCAGGTTT 2 4 0 TATATAACGG 0.750227 -134 AAGGGAAGTTTTAAAGAGTTAAGCAATCTAAAGGGAT 2 94 0 TTAATAACAT 0.789471 -44 AACTTTATTTTTAACTAATAAAACAGTTTGTAGTGTT 5 16 1 TTAATAACGT 0.874554 -146 aacttaagttaaaatcccttaacccaaagccaattta 8 18 0 aaaataacaa 0.650629 -283 gttgtaattattaagttctgaaaccagcgccgtaatt 8 72 1 ttaataacag 0.792582 -229 cacttttttgataaccattcaaaccgtgaccaaattt 8 153 1 ataataacgt 0.943429 -148 ttcaggaggaaaaagtagtaaaacggttaacgattgt 9 16 1 aaaataacgt 0.956451 -71 tttttgccaaaaaagcgcttaaacaagtagttagagt 10 16 0 aaaataacag 0.923301 -106 cttttttggcaaaaactttgaagctggcatcgagctt 10 38 1 aaaataacgg 0.957228 -84 tggtttaagaattacaatttaaacgatattaaat 12 19 1 attataacat 0.74226 -24 aaaccgatttatcacagataaaacaggttttaacttc 13 26 1 atcataacgg 0.761919 -29 aaaaagtataaatctgtatccaacaca 14 1 1 aaaataacgt 0.956451 -300 tagactattgaataaaactaaaacaatcgttattgtg 14 70 1 aatataacat 0.791348 -231 **** * ** * ** Masking position 11 Map Score: 8.08863 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 141 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TGCAATAATGGCAACGAAAATAGAGCTAATA 6 89 1 GCAACGAAAT 0.650801 -27 ttacctttcgccaacgcctttaagttgctgt 7 29 0 ccaacgcctt 0.977812 -48 atcccttaacccaaagccaatttacacgagt 8 11 0 ccaaagccat 0.965259 -290 aggaatgaaagcaaaacctatttcacaagct 8 111 0 gcaaaaccat 0.945719 -190 cgcttttttggcaaaaactttgaagctggca 10 36 1 gcaaaaactt 0.875544 -86 aattcttaaaccaacgccctt 12 1 0 ccaacgcctt 0.977812 -42 aaatctgtatccaacacaattccctaaaaat 14 20 1 ccaacacatt 0.870808 -281 cgtgtttttaccacaaccaatcgttagtaat 14 233 1 ccacaaccat 0.834498 -68 atggaaattcgcaaaaacattgtcacgaaat 15 222 0 gcaaaaactt 0.875544 -79 ******** ** Masking position 3 Map Score: 3.29671 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 78 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 CAGAATGAGTGTGGAATTTGCGTAATTGGT 5 142 1 GAATTTGCGT 0.913365 -20 TCTTTTATTAGCTCTATTTTCGTTGCCATTATT 6 92 0 GTATTTTCGT 0.808649 -24 actcgtgtaaattggctttgggttaag 8 5 1 gaaattggct 0.639246 -296 ttcaaaccgtgaccaaatttcctacgttaacga 8 170 1 gaaatttcct 0.964454 -131 gtcaaaatgaggcaagatgtccttattttcatg 8 249 0 gagatgtcct 0.722593 -52 gataaaacaggttttaacttcgt 13 42 1 gtaacttcgt 0.804674 -13 gtggttttaggtgtagatttcgtttggtttttc 14 104 1 gagatttcgt 0.967381 -197 atttttcggtgggcaatttttgtccactgaaaa 14 132 0 gaatttttgt 0.593969 -169 aaaaggcgaggtcaaaatttcgtcgatgtgaat 15 185 0 gaaatttcgt 0.981478 -116 acctcgcctttttgaaatttcgtgacaatgttt 15 206 1 taaatttcgt 0.791956 -95 atttccattcgacaagactgcgtctcgatctag 15 245 1 gagactgcgt 0.851772 -56 gtgtaataacgaacaaatttcctttccctttcg 15 277 1 gaaatttcct 0.964458 -24 * ********* Masking position 13 Map Score: 4.76912 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 18 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 TTGGTTTTGTGGTTTTTAGCTTGTTTATAA 1 48 1 GGTTTTTAGC 0.943914 -63 GTTTTTAGCTTGTTTATAACAATATTATTG 1 59 1 TGTTTATAAC 0.837377 -52 TAAGTAACTTTATTTTTAACTAATAAAACA 5 11 1 TATTTTTAAC 0.913311 -151 CAGTTTGTAGTGTTTGTAACAGCTTACAAA 5 39 1 TGTTTGTAAC 0.953398 -123 TTAAAATAATTGTTCTTAACT 6 2 0 TGTTCTTAAC 0.848655 -114 ttgggttaagggattttaacttaagttgct 8 28 1 ggattttaac 0.857564 -273 accagcgccgtaattttagcttgtgaaata 8 94 1 taattttagc 0.596523 -207 aaataatccatgtttttagctaatgtaat 9 68 1 tgtttttagc 0.953398 -19 tacttaaattatatttaaccttgcaaa 11 9 0 tatatttaac 0.54961 -19 ttcacaattcggtttgtaacagtaggagga 14 201 0 ggtttgtaac 0.943905 -100 tgtgaaaccgtgtttttaccacaaccaatc 14 225 1 tgtttttacc 0.884148 -76 aaagaccattgatttgtaaccgcggttgaa 15 60 0 gatttgtaac 0.84444 -241 ********** Masking position 8 Map Score: 10.8164 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 153 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 TCAATAAAACTCGATAATAAC 1 2 1 CAATAAAACT 0.838089 -109 TTACATTATGCAGTAAAACTGCAATAATAT 1 80 0 CAGTAAAACT 0.957682 -31 CAGCTTGAAGTAAAATTAATCCTA 3 8 1 AAGTAAAATT 0.752979 -17 ATGACATCTAAAGTAAAACCCTAGCTTATA 4 56 0 AAGTAAAACC 0.939239 -46 aaaggaatgaaagcaaaacctatttcacaa 8 114 0 aagcaaaacc 0.80414 -187 gttatcaaaaaagtgaaacttggaaaagga 8 138 0 aagtgaaact 0.939238 -163 taaacattttgagtgaaactataatcacgc 8 212 0 gagtgaaact 0.927616 -89 gtagactattgaataaaactaaaacaatcg 14 69 1 gaataaaact 0.838089 -232 ********** Masking position 6 Map Score: 3.06662 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 76 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 ACAAGCTAAAAACCACAAAACCAAGGTTTT 1 42 0 AACCACAAAA 0.960029 -69 TATGCAGTAAAACTGCAATAATATTGTTAT 1 74 0 AACTGCAATA 0.764976 -37 AGAAGTTTATAACCACAATAATTTTAAATT 4 15 0 AACCACAATA 0.98221 -87 CAATAATGGCAACGAAAATAGAGCTAATAA 6 91 1 AACGAAAATA 0.816992 -25 ttcctacgttaacgacaaaataaagcgtga 8 188 1 aacgacaaaa 0.926219 -113 ctttcttttcaaccagaatttgcgctt 10 105 1 aaccagaatt 0.724374 -17 ctacacctaaaaccacaataacgattgttt 14 90 0 aaccacaata 0.98221 -211 ********** Masking position 7 Map Score: 3.09606 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 20 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 ttaaattcggacaatcgttaaccgttttac 9 33 0 acaatcgtta 0.976661 -54 taaaactaaaacaatcgttattgtggtttt 14 82 1 acaatcgtta 0.976661 -219 tttaccacaaccaatcgttagtaattaatt 14 239 1 ccaatcgtta 0.984786 -62 ttttcatcgccgaatcgttttctgaaagac 15 84 0 cgaatcgttt 0.905273 -217 ********** Masking position 5 Map Score: 0.971448 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 2 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 13 ********** No masking Map Score: 7.21444e-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 14 ********** No masking Map Score: 7.21444e-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 15 ATTATAAAGGGAAGTTTTAAAGAGTTAAGC 2 107 0 GAAGTTTTAA 0.798684 -31 ACAATAATTTTAAATTTTAA 4 1 0 TAAATTTTAA 0.870442 -101 ggaacgactaaacattttgagtgaaactat 8 220 0 aacattttga 0.775758 -81 gtttaagaattacaatttaaacgatattaa 12 21 1 tacaatttaa 0.675457 -22 aaccacgtattacattttaatgtttcg 14 284 1 tacattttaa 0.9296 -17 taaagtgtgatacgtttcaaccgcggttac 15 45 1 tacgtttcaa 0.75933 -256 gaaaacgcagaacattttaatctcgtagtt 15 109 1 aacattttaa 0.876198 -192 tcacatcgacgaaattttgacctcgccttt 15 187 1 gaaattttga 0.798683 -114 acattgtcacgaaatttcaaaaaggcgagg 15 207 0 gaaatttcaa 0.798684 -94 ********** Masking position 6 Map Score: 0.471425 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 24 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274