AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_mpneu_reg_300.orf -o215_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 Input sequences: #1 RMP00268 300 Mycoplasma_pneumoniae #2 RMP00269 187 Mycoplasma_pneumoniae #3 RMP00272 103 Mycoplasma_pneumoniae #4 RMP00274 121 Mycoplasma_pneumoniae #5 RMP00276 99 Mycoplasma_pneumoniae #6 RMP00278 169 Mycoplasma_pneumoniae #7 RMP00279 213 Mycoplasma_pneumoniae #8 RMP00280 203 Mycoplasma_pneumoniae #9 RMP00512 146 Mycoplasma_pneumoniae #10 RMP00513 23 Mycoplasma_pneumoniae #11 RMP00517 300 Mycoplasma_pneumoniae Motif number 1 ctaatgctaatttcttttaaaccctaaaaaa 1 56 0 tttttttaaa 0.798675 -245 ggttaggaaatttaattgaaaaactaccaca 1 185 0 tttattgaaa 0.674673 -116 gaaaaatatttgtttggaaataacaaata 1 282 0 ttttttggaa 0.895627 -19 ggttgagtgccttattggcaataaacgctta 2 40 1 cttttggcaa 0.83406 -148 ctaaattatttttatttgcactttaagcatt 2 128 1 ttttttgcac 0.974714 -60 cagccctttttttattggcaccttagcctca 3 53 1 tttttggcac 0.955372 -51 gtttaagcgcttttttggcaaaaactttgaa 4 29 1 tttttggcaa 0.978171 -93 ggcatcgagctttgtttgcaaattattaaag 4 63 1 ttttttgcaa 0.987758 -59 agcttgcagctttcttttcaaccagaatttg 4 96 1 tttttttcaa 0.920215 -26 gctggattagtttatttgccattttctccag 7 38 1 ttttttgcca 0.94646 -176 ataatttttgtttatttaaaattcagttatt 7 164 1 ttttttaaaa 0.612008 -50 accaacatgctttttttgaaagctaacttaa 8 16 0 ttttttgaaa 0.965328 -188 atagctgctctttgtttgaacaatctcatgt 8 95 1 ttttttgaac 0.930181 -109 gtcttctgcgtttattcgcactttaatattg 9 73 0 tttttcgcac 0.91796 -74 ataaaacatatttgttttaaatccttggcgt 9 102 0 tttttttaaa 0.79947 -45 gttttatggttttctttgccaaaataacttt 9 126 1 ttttttgcca 0.946459 -21 tattctgtgatttttcggcaaaatcgtcgag 11 80 0 ttttcggcaa 0.907554 -221 tttcgaaatttttttccgcaaatt 11 287 1 ttttccgcaa 0.836899 -14 *** ******* Masking position 3 Map Score: 24.1266 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 122 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 cattaggcttaaaaattaaattttcctgtt 1 81 1 aaaaattaaa 0.781711 -220 ggaaataacaaatacttaaaacaactaaaa 1 266 0 aatacttaaa 0.640927 -35 atatgtggttagtaattaaaactaa 2 6 0 agtaattaaa 0.917551 -182 ttaatctactagtaaataaatcaggcacgc 2 68 1 agtaaataaa 0.82309 -120 atattctaccaattattaacaattagcagt 2 161 0 aattattaac 0.640926 -27 tttgtttgcaaattattaaagacagcttgc 4 73 1 aattattaaa 0.92445 -49 tattaatattaaaaattaaaattttattaa 5 37 1 aaaaattaaa 0.781711 -63 ggcgttttgcgattaataaaattttaattt 5 49 0 gattaataaa 0.772304 -51 aataaacaaaaattattaaaagcaagcgtc 7 150 0 aattattaaa 0.92445 -64 tttaaaattcagttattaaagcaacagcag 7 178 1 agttattaaa 0.917556 -36 caacagcagaggtaaataaagtttt 7 199 1 ggtaaataaa 0.755202 -15 gctgctttttaattaataaacttactaacc 8 129 1 aattaataaa 0.836475 -75 tgcttatgttggttattaaaaccaggttag 8 153 0 ggttattaaa 0.880663 -51 taagcaatacgaaaattaaaaccaagcgag 8 177 1 gaaaattaaa 0.703662 -27 ********** Masking position 8 Map Score: 12.5297 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 89 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 aagtatttgttatttccaaacaaatatttt 1 279 1 tatttccaaa 0.84831 -22 attaagcgtttattgccaataaggcactca 2 43 0 tattgccaat 0.715784 -145 gcttcaaagtttttgccaaaaaagcgctta 4 32 0 ttttgccaaa 0.956388 -90 aaagttattttggcaaagaaaaccata 9 130 0 ttttggcaaa 0.948986 -17 aactcgacgattttgccgaaaaatcacaga 11 78 1 ttttgccgaa 0.988766 -223 aatcacagaatattcgcgaatctttcggaa 11 99 1 tattcgcgaa 0.838803 -202 tttaccgtgtcttttccgaaagattcgcga 11 112 0 cttttccgaa 0.829415 -189 cattcgggggttttgccggacatcccgagt 11 161 0 ttttgccgga 0.95019 -140 ttgttacaattattggcgaacattcggggg 11 181 0 tattggcgaa 0.969172 -120 aacgtcacaattttggcgaaatttcgaata 11 257 1 ttttggcgaa 0.981523 -44 tttcgaaatttttttccgcaaatt 11 287 1 tttttccgca 0.843369 -14 ********** Masking position 4 Map Score: 11.0104 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 80 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 4 ctaatgaaaacggttttaactcgataaatct 1 12 0 cggtttaact 0.956776 -289 ttaattttttagggtttaaaagaaattagca 1 52 1 aggtttaaaa 0.961284 -249 aattagcattaggcttaaaaattaaattttc 1 75 1 aggttaaaaa 0.873449 -226 cacccattaaaggcttaaaaagtttcaacaa 1 144 0 aggttaaaaa 0.873449 -157 ttgcactttaagcatttaactgctaattgtt 2 143 1 agctttaact 0.952956 -45 acaggctttcaataagcagataa 3 3 1 aggtttcaat 0.865537 -101 ttaatgccttaggttttaactttgtcattgc 6 130 1 aggtttaact 0.975363 -40 ttattaacacagcttttaactacaactgctt 7 73 1 agctttaact 0.952953 -141 caggtaagaacgccttcaaatggcttcaaag 7 110 0 cgcttcaaat 0.807823 -104 aaattaagttagctttcaaaaaaagcatgtt 8 13 1 agcttcaaaa 0.845247 -191 gaagacgccaaggatttaaaacaaatatgtt 9 98 1 aggtttaaaa 0.961284 -49 ggatcgaactcggattttactcgggatgtcc 11 143 1 cggttttact 0.73771 -158 *** ******* Masking position 9 Map Score: 9.80857 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 76 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 aattatttttatttgcactttaagcattta 2 131 1 atttgcactt 0.962767 -57 ccctttttttattggcaccttagcctcatt 3 56 1 attggcacct 0.830146 -48 ttcaaccagaatttgcgctt 4 112 1 atttgcgctt 0.984561 -10 ccttgaggcgttttgcgattaataaaattt 5 55 0 ttttgcgatt 0.919379 -45 caagctggagttttgcgctttgcggttgat 6 29 0 ttttgcgctt 0.958166 -141 ggattagtttatttgccattttctccagtg 7 41 1 atttgccatt 0.868621 -173 ttctgcgtttattcgcactttaatattgtt 9 71 0 attcgcactt 0.933541 -76 ccaattctctatttgcgacttacgaaaaac 11 30 0 atttgcgact 0.906027 -271 atcacagaatattcgcgaatctttcggaaa 11 100 1 attcgcgaat 0.482489 -201 ********** Masking position 3 Map Score: 6.97468 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 44 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 6 gggtgttgaaaagtttgtggtagtttttcaatta 1 170 1 aagttggtat 0.899151 -131 caggcacgctaatttagcagcactatttcggtag 2 89 1 aatttggcat 0.969613 -99 aaataaaaataatttagcaacactaccgaaatag 2 111 0 aatttgacat 0.968284 -77 tagcgctataaagttcgttatattaatattaaaa 5 17 1 aagttgatat 0.939947 -83 attattggacaattttgttacaattattggcgaa 11 191 0 aatttgacat 0.982536 -110 tacctcggaaaattttgttacaattattggacaa 11 213 0 aatttgacat 0.982536 -88 aaatattcgaaatttcgccaaaattgtgacgttt 11 256 0 aatttgaaat 0.714195 -45 tgcggaaaaaaatttcgaaatattcgaaatttcg 11 273 0 aatttgatat 0.956266 -28 ***** * *** * Masking position 12 Map Score: 7.68601 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 9 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 7 taatttcttttaaaccctaaaaaattaattg 1 49 0 taaacctaaa 0.944599 -252 gcattaggcttaaaaattaaattttcctgtt 1 80 1 taaaattaaa 0.709408 -221 gtttcaacaataaaaactaaaaactctacgc 1 123 0 taaaactaaa 0.933867 -178 caacacccattaaaggcttaaaaagtttcaa 1 147 0 taaagcttaa 0.929029 -154 ttggaaataacaaatacttaaaacaactaaa 1 267 0 caaaacttaa 0.746516 -34 ttattggcaataaacgcttaatctactagta 2 51 1 taaagcttaa 0.944236 -137 aattagcagttaaatgcttaaagtgcaaata 2 140 0 taaagcttaa 0.944236 -48 atattaatattaaaaattaaaattttattaa 5 36 1 taaaattaaa 0.709408 -64 atgacaaagttaaaacctaaggcattaattt 6 127 0 taaacctaag 0.879977 -43 atatttgttttaaatccttggcgtcttctgc 9 95 0 taaaccttgg 0.604576 -52 **** ****** Masking position 4 Map Score: 4.7157 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 91 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 aggaaaatttaatttttaagcctaatgctaa 1 77 0 aattttaagc 0.714618 -224 aactaccacaaacttttcaacacccattaaa 1 164 0 aactttcaac 0.710517 -137 ttttcaattaaatttcctaaccaagatacga 1 194 1 aatttctaac 0.914962 -107 aagtatttgttatttccaaacaaatattttt 1 279 1 tatttcaaac 0.605583 -22 caggcacgctaatttagcagcactatttcgg 2 89 1 aatttgcagc 0.914756 -99 aaataaaaataatttagcaacactaccgaaa 2 114 0 aatttgcaac 0.950483 -74 ttttggcaaaaactttgaagctggcatcgag 4 41 1 aacttgaagc 0.85956 -81 tgtctttaataatttgcaaacaaagctcgat 4 66 0 aatttcaaac 0.929854 -56 ttaattaataaacttactaacctggttttaa 8 137 1 aacttctaac 0.85745 -67 attattggacaattttgttacaattattggc 11 194 0 aatttgttac 0.780769 -107 tacctcggaaaattttgttacaattattgga 11 216 0 aatttgttac 0.780769 -85 tgcggaaaaaaatttcgaaatattcgaaatt 11 276 0 aatttgaaat 0.584223 -25 ***** ***** Masking position 2 Map Score: 4.74546 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 102 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 aattttcctgttatgccagtgatggcgtagagt 1 99 1 ttatgcgtgt 0.944595 -202 gttgaaaagtttgtggtagtttttcaattaaat 1 174 1 ttgtgggttt 0.905711 -127 gcactcaaccttgtatatgtggttagtaattaa 2 17 0 ttgtatgtgt 0.96333 -171 attgggtcatttatgtaagtgataaagcccc 3 83 1 ttatgtgtgt 0.979004 -21 tactacatcattgtgtgggtgttattaggggaa 6 96 1 ttgtgtgtgt 0.989723 -74 ttgtcagtttttgtattagtgctggattagttt 7 18 1 ttgtatgtgt 0.96333 -196 ttcgtattgcttatgttggttattaaaaccagg 8 157 0 ttatgtgttt 0.927112 -47 ****** *** * Masking position 4 Map Score: 3.30721 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 = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 tcagcattggttttttagttgttttaagtatttg 1 254 1 ttttgttgtt 0.958677 -47 agtacagccctttttttattggcaccttagcctc 3 49 1 ttttattgca 0.657797 -55 gagttttgcgctttgcggttgattgaaaaaactg 6 18 0 ctttgttgtt 0.973682 -152 taggttttaactttgtcattgccccaaataaccg 6 139 1 ctttattgcc 0.893176 -31 ctttatttacctctgctgttgctttaataactga 7 186 0 ctctgttgtt 0.885263 -28 tacatggtccctttatggttgcctgtttccccgt 8 46 1 ctttgttgct 0.975659 -158 ttggttttaattttcgtattgcttatgttggtta 8 168 0 ttttattgtt 0.908262 -36 tttattcgcactttaatattgtttaattggggac 9 60 0 ctttattgtt 0.940436 -87 aacaaatatgttttatggttttctttgccaaaat 9 117 1 ttttgtttct 0.812911 -30 ggtattctgttttttatgtttttcgtaagtcgca 11 13 1 ttttgttttc 0.662204 -288 **** **** ** Masking position 9 Map Score: 2.0625 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 148 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 ttcttttaaaccctaaaaaattaattggac 1 46 0 ccctaaaaaa 0.873459 -255 gcattaatttcccctaataacacccacaca 6 107 0 cccctaataa 0.964819 -63 tttgtcattgccccaaataaccgtacttta 6 150 1 ccccaaataa 0.985774 -20 ctgaaatcgtccccaattaaacaatattaa 9 52 1 ccccaattaa 0.964819 -95 ********** Masking position 6 Map Score: 0.18048 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 12 ********** No masking Map Score: 1.89958e-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 ********** No masking Map Score: 1.89958e-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: 1.89958e-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