AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_mpneu_reg_100.orf -o199_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: RMP00396 22 Mycoplasma_pneumoniae RMP00371 18 Mycoplasma_pneumoniae Input sequences: #1 RMP00178 84 Mycoplasma_pneumoniae #2 RMP00304 37 Mycoplasma_pneumoniae #3 RMP00305 117 Mycoplasma_pneumoniae #4 RMP00326 300 Mycoplasma_pneumoniae #5 RMP00327 92 Mycoplasma_pneumoniae #6 RMP00368 300 Mycoplasma_pneumoniae #7 RMP00394 116 Mycoplasma_pneumoniae #8 RMP00395 63 Mycoplasma_pneumoniae #9 RMP00590 273 Mycoplasma_pneumoniae #10 RMP00604 56 Mycoplasma_pneumoniae #11 RMP00605 22 Mycoplasma_pneumoniae #12 RMP00606 53 Mycoplasma_pneumoniae #13 RMP00607 28 Mycoplasma_pneumoniae #14 RMP00613 55 Mycoplasma_pneumoniae #15 RMP00617 275 Mycoplasma_pneumoniae #16 RMP00668 93 Mycoplasma_pneumoniae #17 RMP00669 246 Mycoplasma_pneumoniae Motif number 1 taattggacgttatttggtttcttttattgctcaaaaattga 3 31 1 ttagtttttt 0.810377 -87 ctattaggagctattgaaaaaatttcaatttttgagcaataa 3 55 0 ctaatttctt 0.799067 -63 ttcattgatttttgcttgtgctttttccttataaaactcatc 4 101 0 tttgtttttt 0.878 -200 ttccttaattcttgagcttttctttctttgatcaacttaata 4 145 0 cttttttctt 0.881182 -156 gaaaacttaatttaatttttagttttcttttttgcaaccaat 4 217 0 tttttttttt 0.954056 -84 tttctccgctttaattaacaattttcttttatataaatagga 4 255 1 ttaatttctt 0.884483 -46 ccttttgtcgctgttagtggctttttactgttatttttagcc 5 46 1 ctgttttttt 0.757833 -47 ccacgccttctttatctttttgtttccgtattaccccctaaa 7 42 1 tttttttctt 0.934574 -75 cctatcgttatttggctactaatttgtttcctaacggtaatg 9 70 0 tttatttgtt 0.912385 -204 gttctaaacctttaaaaagcgttttggtttctggcgccttaa 9 151 1 tttatttgtt 0.912385 -123 gcgttttactttttgattgggattttattctttttcgtgatg 9 226 0 tttttttttt 0.954056 -48 gaaatacccttttgatttatattttcatttctaaatacggat 10 20 0 tttttttctt 0.934574 -37 actaactcaattacaaaaagcatttttttccttaaattctat 12 11 0 ttaatttttt 0.917594 -43 aatcaccaagttttgtaagatgtttttttgctatgatcattc 15 14 0 tttatttttt 0.949371 -262 ttacgacaaactgaggctcacctttggctaatatttagcgca 15 75 1 ctgttttgtt 0.634755 -201 cttgtgaaagcttatgattattttttctttttccttggacca 15 205 0 cttttttttt 0.915119 -71 aattcccactttaaactaccagttttactgatgcgaaaagcc 16 52 0 ttaatttttt 0.917594 -42 tctgggtaaattaacaattttctttgaatgattgtcgttttt 17 58 0 ttattttgtt 0.87258 -189 gtaactttaatttgttgaagttttttcatcattggggcgaaa 17 127 0 tttatttttt 0.949371 -120 caaattaaagttactaatacccttttattattccggacgttc 17 155 1 ttattttttt 0.924988 -92 acgttcgccgtttgatcaaacctttttctattccttaatcag 17 191 1 tttatttttt 0.94937 -56 *** * **** * * Masking position 13 Map Score: 24.9113 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 213 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 aacgttatcgtgtttgctactattaggagctattg 3 81 0 tgtttgccta 0.946866 -37 ttaaattaagttttctccgctttaattaacaattt 4 244 1 ttttctccta 0.757714 -57 gcatgcggcccttttgtcgctgttagtggcttttt 5 37 1 cttttgtcta 0.922282 -56 cttctttatctttttgtttccgtattaccccctaa 7 48 1 tttttgtctt 0.80095 -69 ctaacggtaatgtttgtaatgataaacttaacgca 9 47 0 tgtttgttta 0.599877 -227 tagaactggactttcgcttcgttcaggcggtcatc 9 122 0 ctttcgccta 0.937156 -152 agcgttttggtttctggcgccttaacagttttaag 9 168 1 tttctggcta 0.759134 -106 gtgatgattttatttgtagcattaaacctcttaaa 9 197 0 tatttgtcta 0.825095 -77 tttctgtcgcgcttataacattgtg 13 14 0 tttctgtcta 0.922218 -15 gtaagatgtttttttgctatgatcattcatg 15 7 0 tttttgctta 0.867664 -269 aaatcagcgatttttgtaacaatcaccaagttttg 15 41 0 tttttgtcta 0.970279 -235 cctatgtggcttttcgcatcagtaaaactggtagt 16 45 1 ttttcgccta 0.980676 -49 cgaggttcgattttcgtaaccctgaacaaacgcga 17 22 0 ttttcgtcta 0.973812 -225 ttctagcggtttttcgccccaatgatgaaaaaact 17 116 1 ttttcgccta 0.98077 -131 ******* * * * Masking position 3 Map Score: 10.9486 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 83 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 ggtttcttttattgctcaaaaattgaaatt 3 47 1 attgctcaaa 0.551741 -71 atataccacctttgatcacgataaaagaga 4 43 1 tttgatcacg 0.963392 -258 cttttctttctttgatcaacttaataagtt 4 141 0 tttgatcaac 0.707974 -160 acgaacaaagtttgctcaagcaactcatgc 6 40 1 tttgctcaag 0.936368 -261 acaattaaaatttgattacga 9 2 0 tttgattacg 0.871776 -272 cgttttactttttgattgggattttattct 9 237 0 tttgattggg 0.848411 -37 tttattgattgagataagagat 11 10 0 attgattgag 0.778716 -13 attattgcgatttgatcgagggtgttaaac 14 25 0 tttgatcgag 0.963311 -31 tctaaactacattggtcaggttgattttca 15 135 0 attggtcagg 0.788776 -141 tgccgaattgatcgcgtttgttcagg 17 7 1 attgatcgcg 0.92931 -240 attgatcgcgtttgttcagggttacgaaaa 17 17 1 tttgttcagg 0.82919 -230 acgttcgccgtttgatcaaacctttttcta 17 191 1 tttgatcaaa 0.489046 -56 ********** Masking position 6 Map Score: 5.836 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 114 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 tgtagagaggcttataattcttggagtagtg 1 19 0 cttataatct 0.929303 -66 gtgctttttccttataaaactcatcagtagc 4 95 0 cttataaact 0.954725 -206 taacgcggaacttacaattgttagtatgagc 7 86 1 cttacaatgt 0.927976 -31 gttaactttgattataaaactttctttaagg 8 13 0 attataaact 0.673976 -51 gaaaaaagagcttacaaaagtgtaagcatgg 8 43 0 cttacaaagt 0.953852 -21 cattaaacctcttaaaactgttaaggcgcca 9 182 0 cttaaaatgt 0.764311 -92 ttctgtcgcgcttataacattgtgtta 13 7 0 cttataaatt 0.80162 -22 aaaaaaacatcttacaaaacttggtgattgt 15 27 1 cttacaaact 0.953852 -249 gtccattggtcttataatcgtacgactccct 15 167 1 cttataacgt 0.885196 -109 ******* *** Masking position 6 Map Score: 4.76044 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 16 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 aaaatataaatgaataattaataaata 2 21 0 aataaaaaaa 0.822669 -17 tcaatttttgagcaataaaagaaaccaaataacgtcc 3 36 0 aaaaaaaaca 0.857015 -82 acctttgatcacgataaaagagaataactgcaagctg 4 50 1 aaaaagaaaa 0.96369 -251 gatgagttttataaggaaaaagcacaagcaaaaatca 4 101 1 aaaaaacaaa 0.66236 -200 gaaaagctcaagaattaaggaaaagtaatgaggagtg 4 165 1 aaaaggaata 0.764757 -136 attggttgcaaaaaagaaaactaaaaattaaattaag 4 217 1 aaaaaaaaaa 0.94279 -84 ttatataaataggatcaaagataaaaaa 4 283 1 aaaaagaaaa 0.96369 -18 tcgtgtacaaaaaagggctaaaaataacagtaa 5 70 0 aaaaggtaaa 0.740413 -23 gattttgacgaaaacttaaacgaacaaagtttgctca 6 21 1 aataaaaaaa 0.822669 -280 ttaccctagaaccaacaagggaaacaataacagttcc 6 85 1 aaaaggaaaa 0.952694 -216 ggcgaattagatcagttagagaaagaacaatcaattc 6 156 1 aatagaaaaa 0.778769 -145 caccatatctaccataaagtgaaaaaaattgcgaatt 6 188 0 aaaagtaaaa 0.637612 -113 gtaatacggaaacaaaaagataaagaaggcgtggtac 7 39 0 aaaagaaaaa 0.92595 -78 agaaagttttataatcaaagttaaccatgcttacact 8 19 1 aaaaagaaca 0.906132 -45 aaataaaatcatcacgaaaaagaataaaatcccaatc 9 217 1 aaaaaaaaaa 0.94279 -57 atagaatttaaggaaaaaaatgctttttg 12 3 1 aataagaaaa 0.881959 -51 catgaatgatcatagcaaaaaaacatcttaca 15 6 1 aaatagaaaa 0.655039 -270 ggtccaaggaaaaagaaaaaataatcataagctttca 15 206 1 aaaaaaaaca 0.857015 -70 aacgtccggaataataaaagggtattagtaactttaa 17 159 0 aaaaagtata 0.377644 -88 * * **** ** ** Masking position 4 Map Score: 19.9568 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 163 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 agttttctccgctttaattaacaattttcttttat 4 252 1 gctataacat 0.970704 -49 acaaaaaagggctaaaaataacagtaaaaagccac 5 62 0 gcaataacat 0.984081 -31 aaccaacaagggaaacaataacagttcccctagaa 6 94 1 ggaataacat 0.984084 -207 taacaccgccgctcatactaacaattgtaagttcc 7 92 0 gcaataacat 0.98408 -25 gaaattttctgggtaaattaacaattttctttgaa 17 72 0 ggaataacat 0.984084 -175 ataataaaagggtattagtaactttaatttgttga 17 151 0 ggtataactt 0.890934 -96 ** * * ***** * Masking position 7 Map Score: 2.11145 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 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 7 aaggaaaagtaatgaggagtgggttgctaaagc 4 181 1 aaagggtggg 0.9861 -120 ctttatggtagatatggtgtggtcaaaagccaa 6 206 1 gatgggtggt 0.968533 -95 ttaacacatcaacatggggttggcttttgacca 6 225 0 aatgggttgg 0.978131 -76 gcggtttatgaacttggagttggttagcgaagt 6 261 0 aatgggttgg 0.978131 -40 caaaaagataaagaaggcgtggtacttagtttt 7 31 0 aaagggtggt 0.978316 -86 tcaaatcgcaataatggtgtggttaa 14 40 1 attgggtggt 0.95406 -16 ** *** ***** Masking position 10 Map Score: 2.06332 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 aaatgaataattaataaatactccccaaat 2 11 0 ttaataaata 0.669022 -27 aaaatataaatgaataattaataaat 2 22 0 taaatgaata 0.857882 -16 aaattaaatcaatacaataataat 3 5 1 taaatcaata 0.681087 -113 gtctttaataaaaacgttatcgtg 3 104 0 ttaataaaaa 0.747431 -14 gatgagttttataaggaaaaagcacaagca 4 101 1 ataaggaaaa 0.700944 -200 agctcaagaattaaggaaaagtaatgagga 4 169 1 ttaaggaaaa 0.943367 -132 cctatttatataaaagaaaattgttaatta 4 266 0 taaaagaaaa 0.68556 -35 aatgaaaatataaatcaaaagggtatttca 10 33 1 taaatcaaaa 0.757673 -24 atagaatttaaggaaaaaaatgctttt 12 8 1 ttaaggaaaa 0.943367 -46 acttgactgattaaggaatagaaaaaggtt 17 209 0 ttaaggaata 0.91921 -38 ********** Masking position 4 Map Score: 2.62317 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 170 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 agtagcaaacacgataacgtttttattaaagac 3 95 1 agtacgtttt 0.911503 -23 gttctagggtaatgttacgggttttgggcatga 6 64 0 attacgggtt 0.869488 -237 tacgttctacaatgttacgttctaggggaactg 6 115 0 attacgttct 0.722542 -186 gttagatcaacggtttgcggtttatgaacttgg 6 277 0 cgtgcggttt 0.897575 -24 gacaatctaaaatttcgcgttttactttttgat 9 251 0 attgcgtttt 0.952183 -23 taaccacaccattattgcgatttgatcgagggt 14 32 0 attgcgattt 0.932873 -24 gcgattgtgacggtttgggtttgcaa 15 260 0 attacggttt 0.969647 -16 tcactgtgttattctagcggtttttcgccccaa 17 105 1 attgcggttt 0.980748 -142 attattccggacgttcgccgtttgatcaaacct 17 181 1 agtgccgttt 0.844748 -66 agtcaagttaacactgacgattttcg 17 231 1 aatacgattt 0.644021 -16 * * * ******* Masking position 5 Map Score: 2.20582 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 63 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 tgggttgctaaagcgaaattggttgcaaaaaa 4 200 1 aagcaaatgg 0.917784 -101 tatttatataaaagaaaattgttaattaaagc 4 262 0 aaagaaatgt 0.809091 -39 caaactttacaaagcccattagcatgcggccc 5 16 1 aaagccatag 0.749845 -77 atttagcgcaaagggacatcggtagacgtgaa 15 107 1 aaggacatgg 0.978931 -169 tggactttctaaactacattggtcaggttgat 15 140 0 aaacacatgg 0.966817 -136 tgtagtttagaaagtccattggtcttataatc 15 154 1 aaagccatgg 0.964084 -122 ctgatgcgaaaagccacataggtgaagctggt 16 35 0 aagcacatgg 0.966169 -59 acaatcattcaaagaaaattgttaatttaccc 17 65 1 aaagaaatgt 0.809091 -182 **** **** ** Masking position 8 Map Score: 2.33433 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 22 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 ********** No masking Map Score: -6.41377e-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: -6.41377e-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 13 tataagcctctctacagctttatctcaaact 1 34 1 tctaagcttt 0.96872 -51 tgaaattttttcaatagctcctaatagtagc 3 70 1 tcaaagctcc 0.860923 -48 ataaaactcatcagtagctcttctaacagct 4 82 0 tcagagctct 0.83121 -219 tttccttaattcttgagcttttctttctttg 4 157 0 tcttagcttt 0.959651 -144 tctagaccttcaaactattaa 7 1 1 tctaaccttc 0.880952 -116 taccacgccttctttatctttttgtttccgt 7 40 1 tcttatcttt 0.786297 -77 aaagtccagttctaaacctttaaaaagcgtt 9 143 1 tctaaccttt 0.928916 -131 gaaaaaataatcataagctttcacaagttca 15 220 1 tcatagcttt 0.936812 -56 **** ****** Masking position 6 Map Score: 1.19673 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 41 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 14 ********** No masking Map Score: -6.41377e-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: -6.41377e-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