AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_mpneu_reg_300.orf -o294_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: RMP00673 25 Mycoplasma_pneumoniae Input sequences: #1 RMP00207 76 Mycoplasma_pneumoniae #2 RMP00208 300 Mycoplasma_pneumoniae #3 RMP00212 86 Mycoplasma_pneumoniae #4 RMP00268 300 Mycoplasma_pneumoniae #5 RMP00269 187 Mycoplasma_pneumoniae #6 RMP00272 103 Mycoplasma_pneumoniae #7 RMP00274 121 Mycoplasma_pneumoniae #8 RMP00287 27 Mycoplasma_pneumoniae #9 RMP00288 42 Mycoplasma_pneumoniae #10 RMP00296 54 Mycoplasma_pneumoniae #11 RMP00624 300 Mycoplasma_pneumoniae #12 RMP00677 300 Mycoplasma_pneumoniae Motif number 1 gtttcagaacttaataattacaactcgaactta 2 63 0 ttaattacaa 0.944176 -238 catggattatttataatttaaattcggacaatc 3 47 0 ttaattaaat 0.967955 -40 aattaattttttagggtttaaaagaaattagca 4 50 1 ttagttaaaa 0.832119 -251 agcattaggcttaaaaattaaattttcctgtta 4 79 1 ttaattaaat 0.97194 -222 ttgtggtagtttttcaattaaatttcctaacca 4 184 1 tttattaaat 0.827906 -117 gtatatgtggttagtaattaaaactaa 5 5 0 ttaattaaaa 0.959502 -183 ttattaacaattagcagttaaatgcttaaagtg 5 146 0 ttaattaaat 0.972061 -42 ggggctttatcacttacataaatgaccca 6 85 0 ttaattacat 0.961174 -19 gggcgttggtttaagaattacaatttaaacgat 9 13 1 ttaattacaa 0.944176 -30 caaccaatcgttagtaattaattcaattgaacg 11 246 1 ttaattaatt 0.830401 -55 *** * ****** Masking position 8 Map Score: 9.78402 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 28 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 cgccaacgcctttaagttgctgttacattttgtgcctgatt 1 11 0 tttgctattt 0.713932 -66 gcgccgtaattttagcttgtgaaataggttttgctttcatt 2 98 1 tttgtatttt 0.979022 -203 ctttcattccttttccaagtttcacttttttgataaccatt 2 131 1 tttgtacttt 0.915993 -170 tagatttatcgagttaaaaccgttttcattagcga 4 5 1 tttgtaattt 0.960325 -296 aaccgttttcattagcgagtccaattaattttttagggttt 4 28 1 attgtatttt 0.905049 -273 gagtttttagtttttattgttgaaactttttaagcctttaa 4 128 1 tttgtaattt 0.960325 -173 agcattggttttttagttgttttaagtatttgttatttcca 4 256 1 tttgtaattt 0.960325 -45 gtgctgctaaattagcgtgcctgatttatttactagtagat 5 71 0 attgcatttt 0.827937 -117 tttgcaaggttaaatataatttaagta 8 1 1 tttgtatatt 0.905049 -27 gttattgtggttttaggtgtagatttcgtttggtttttcag 11 98 1 tttgtttttt 0.905049 -203 taatacgtggtttgtctcgttcaattgaattaattactaac 11 255 0 tttgtatatt 0.905049 -46 agcaattagattggtaaagtgtgatacgtttcaaccgcggt 12 31 1 ttggtatttt 0.880393 -270 atgttctgcgttttcatcgccgaatcgttttctgaaagacc 12 83 0 tttgcatttt 0.959282 -218 *** ** ** *** Masking position 2 Map Score: 11.3376 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 45 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 cgacaaaataaagcgtgattatagtttcactcaaaat 2 200 1 aactttattt 0.974208 -101 gacaatcgttaaccgttttactactttttcctcctga 3 17 0 aactttattt 0.974191 -70 taaaacggttaacgattgtccgaatttaaattataaa 3 34 1 aagttgattt 0.974814 -53 tttaatttttaagcctaatgctaatttcttttaaacc 4 64 0 aactttattt 0.974282 -237 tttattgttgaaactttttaagcctttaatgggtgtt 4 140 1 aacttgcttt 0.869156 -161 tgggtgttgaaaagtttgtggtagtttttcaattaaa 4 169 1 aagtttattt 0.969754 -132 tttgcaaggttaaatataatttaagta 8 6 1 aagtatattt 0.880833 -22 aaaccacaataacgattgttttagttttattcaatag 11 74 0 aagtttattt 0.979122 -227 atttcgtgacaatgtttttgcgaatttccattcgaca 12 222 1 aagttgattt 0.9748 -79 ** * * * ** *** Masking position 6 Map Score: 8.16121 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 26 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 agtcgttccatgaaaataaggacatcttgcc 2 241 1 tgaaaaaagg 0.928704 -60 aagcgtttattgccaataaggcactcaacct 5 39 0 tgccaaaagg 0.982954 -149 atgcttaaagtgcaaataaaaataatttagc 5 127 0 tgcaaaaaaa 0.950879 -61 gaggctaaggtgccaataaaaaaagggctgt 6 52 0 tgccaaaaaa 0.958977 -52 tcaaagtttttgccaaaaaagcgcttaaaca 7 28 0 tgccaaaaag 0.988465 -94 tttaataatttgcaaacaaagctcgatgcca 7 62 0 tgcaaaaaag 0.986104 -60 aaattctggttgaaaagaaagctgcaagctg 7 95 0 tgaaaaaaag 0.950879 -27 ****** **** Masking position 6 Map Score: 7.4215 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 25 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 cgttggcgaaaggtaattttattaaattgc 1 44 1 aggtaatttt 0.873256 -33 tcgttaacgtaggaaatttggtcacggttt 2 173 0 aggaaatttg 0.967117 -128 ctggcataacaggaaaatttaatttttaag 4 88 0 aggaaaattt 0.873256 -213 tatcttggttaggaaatttaattgaaaaac 4 192 0 aggaaattta 0.915128 -109 ttgacgttcgaggaattattaagaataatt 11 172 1 aggaattatt 0.81358 -129 taacagtaggaggaattattcttaataatt 11 185 0 aggaattatt 0.81358 -116 attcacatcgacgaaattttgacctcgcct 12 185 1 acgaaatttt 0.930131 -116 aaacattgtcacgaaatttcaaaaaggcga 12 209 0 acgaaatttc 0.829574 -92 cgaaagggaaaggaaatttgttcgttatta 12 280 0 aggaaatttg 0.967117 -21 ********** Masking position 5 Map Score: 6.34866 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 15 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 taaaattacctttcgccaacgcctttaagttgc 1 32 0 ttcccacgcc 0.988186 -45 ttaaaatcccttaacccaaagccaatttacacg 2 14 0 ttaccaagcc 0.985138 -287 tattaagttctgaaaccagcgccgtaattttag 2 80 1 tgaccacgcc 0.99098 -221 ggaaaaggaatgaaagcaaaacctatttcacaa 2 114 0 tgagcaaacc 0.863221 -187 ttactactttttcctcctgaacctta 3 4 0 ttccctaacc 0.912663 -83 ctttttttattggcaccttagcctcattgggtc 6 58 1 tgccctagcc 0.963547 -46 attgtaattcttaaaccaacgccctt 9 4 0 ttaccacgcc 0.988418 -39 agtataaatctgtatccaacacaattccctaaa 11 15 1 tgaccacaca 0.845729 -286 gaaaccgtgtttttaccacaaccaatcgttagt 11 228 1 tttccaaacc 0.892741 -73 ** * *** **** Masking position 1 Map Score: 5.6009 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 101 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 cgtgtaaattggctttgggttaagggatttt 2 14 1 ggctttggtt 0.95449 -287 ctaaaattacggcgctggtttcagaacttaa 2 82 0 ggcgctgttt 0.972342 -219 ttgtgaaataggttttgctttcattcctttt 2 114 1 ggttttgttt 0.937853 -187 tgccagtgatggcgtagagtttttagttttt 4 112 1 ggcgtaggtt 0.970968 -189 aagggcgttggtttaagaattaca 9 4 1 ggcgttgttt 0.991323 -39 tgtggttttaggtgtagatttcgtttggttt 11 103 1 ggtgtagttt 0.960104 -198 cgaacgtcaaggtgttaatttttcggtgggc 11 151 0 ggtgttattt 0.877683 -150 ******* *** Masking position 10 Map Score: 4.99482 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 52 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 aatgaaagcaaaacctatttcacaagctaa 2 109 0 aaacctattt 0.914812 -192 ggacaatcgttaaccgttttactacttttt 3 25 0 taaccgtttt 0.88571 -62 tatcgagttaaaaccgttttcattagcgag 4 17 1 aaaccgtttt 0.680841 -284 atggcaatataaaccgatttatcacagata 10 16 1 aaaccgattt 0.680841 -39 acgaagttaaaacctgttttatctgtgat 10 36 0 aaacctgttt 0.627354 -19 ctactgttacaaaccgaattgtgaaaccgt 11 206 1 aaaccgaatt 0.897832 -95 ccgaattgtgaaaccgtgtttttaccacaa 11 219 1 aaaccgtgtt 0.919572 -82 ********** Masking position 3 Map Score: 6.87546 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 46 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 agcgccgtaattttagcttgtgaaataggtt 2 97 1 ttttagctgt 0.845174 -204 ccaattaattttttagggtttaaaagaaatt 4 48 1 ttttaggttt 0.817904 -253 aaatttaatttttaagcctaatgctaatttc 4 73 0 tttaagctaa 0.693354 -228 ggcgtagagtttttagtttttattgttgaaa 4 122 1 ttttagtttt 0.842369 -179 gttgaaactttttaagcctttaatgggtgtt 4 146 1 tttaagcttt 0.980988 -155 ttttagttgttttaagtatttgttatttcca 4 266 1 tttaagtttt 0.921886 -35 ttactagtagattaagcgtttattgccaata 5 52 0 attaagcttt 0.87894 -136 ttatttgcactttaagcatttaactgctaat 5 139 1 tttaagcttt 0.980988 -49 taactacttgtttaagcgcttttttggcaaa 7 20 1 tttaagcctt 0.914971 -102 agggcgttggtttaagaattacaatttaaac 9 12 1 tttaagatta 0.650405 -31 ******* *** Masking position 5 Map Score: 5.12691 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 131 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 ataagtccgcaatttaataaaattaccttt 1 52 0 aatttaataa 0.870551 -25 ttacaactcgaacttaacaaaagcaactta 2 49 0 aacttaacaa 0.969035 -252 ctggtttcagaacttaataattacaactcg 2 69 0 aacttaataa 0.913605 -232 aacttaacaaaactacgatg 2 291 0 aacttaacaa 0.969035 -10 caggcacgctaatttagcagcactatttcg 5 89 1 aatttagcag 0.857816 -99 aaataaaaataatttagcaacactaccgaa 5 115 0 aatttagcaa 0.942857 -73 ********** Masking position 5 Map Score: 2.25577 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 46 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 gttacattttgtgcctgatt 1 1 0 gtgcctgatt 0.989778 -76 taaggacatcttgcctcattttgacttgac 2 257 1 ttgcctcatt 0.977261 -44 acaaggttgagtgccttattggcaataaac 5 36 1 gtgccttatt 0.972603 -152 ctaaattagcgtgcctgatttatttactag 5 76 0 gtgcctgatt 0.989778 -112 attggcaccttagcctcattgggtcattta 6 66 1 tagcctcatt 0.928889 -38 ********** Masking position 6 Map Score: 4.93099 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 3 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 12 tcattagcgagtccaattaattttttagggt 4 36 1 gtccaataat 0.865637 -265 aatgcttaaagtgcaaataaaaataatttag 5 128 0 gtgcaataaa 0.740061 -60 ttattcaatagtctacataaatgtacctatc 11 54 0 gtctactaaa 0.875648 -247 ggcaatttttgtccactgaaaaaccaaacga 11 123 0 gtccacgaaa 0.973353 -178 gacaaaaattgcccaccgaaaaattaacacc 11 141 1 gcccacgaaa 0.977834 -160 cgtagttgatgcccacctaaatcgcgtttgt 12 132 1 gcccactaaa 0.984975 -169 tgatggtccagcccccataataaattcacat 12 162 1 gccccctaat 0.897703 -139 ****** **** Masking position 9 Map Score: 1.05854 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 27 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 tttccaagtttcacttttttgataaccattc 2 142 1 tcactttttg 0.81018 -159 tgaccttccatcgtagttttgttaagtt 2 283 1 tcgtgttttg 0.941911 -18 gcactcaaccttgtatatgtggttagtaatt 5 19 0 ttgttatgtg 0.609757 -169 acttgtttaagcgcttttttggcaaaaactt 7 25 1 gcgctttttg 0.910328 -97 actaaaacaatcgttattgtggttttaggtg 11 86 1 tcgtattgtg 0.904117 -215 cccacctaaatcgcgtttgtgatggtccagc 12 143 1 tcgctttgtg 0.983773 -158 ggtcaaaatttcgtcgatgtgaatttattat 12 178 0 tcgtgatgtg 0.90399 -123 aattttgacctcgcctttttgaaatttcgtg 12 199 1 tcgctttttg 0.974504 -102 **** ****** Masking position 8 Map Score: 1.90771 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 61 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 14 ********** No masking Map Score: 1.82853e-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 ********** No masking Map Score: 1.82853e-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