AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -ilexA_mpneu_opreg_100.orf -g0.400 -x5 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 = 0 Input sequences: #1 rpsO 157 ribosomal protein S15; similar to Swiss-Prot Accession Number P05766, from B. stearothermophilus #2 1673888 45 MG422 homolog, from M. genitalium #3 1673980 300 G12_orf140b Protein #4 recA 73 recombination protein RecA #5 ctaD 300 cytochrome C oxidase polypeptide I homolog; similar to Swiss-Prot Accession Number P24010, from B. subtilis #6 1674068 88 MG319 homolog, from M. genitalium #7 1674099 184 P115 protein homolog; similar to GenBank Accession Number JQ0894, from M. hyorhinis #8 mutB1 62 DNA helicase II; similar to GenBank Accession Number H64188, from H. influenzae #9 1674192 243 MG241 homolog, from M. genitalium #10 rpsB 300 ribosomal protein S2; similar to Swiss-Prot Accession Number P34831, from S. platensis Motif number 1 GTCCTCATTTTTTCTCTAATAACTGTCAA 3 8 1 TTTTTTTCTA 0.938885 -293 AATCATTGTCTTTTTTGTACTAGCTTCAATCA 3 152 1 TTTTTTTACA 0.822041 -149 AACGCCTGTGTTTTTTGAATTATTTACCTGTT 3 192 1 TTTTTTAATA 0.966751 -109 ACTACGTTTCTTTTTTTGAACAGGTAAATAAT 3 210 0 TTTTTTGAAA 0.787089 -91 AGCGCCAAACTTTTTTATTTGACTACGTTTCT 3 231 0 TTTTTTTTTA 0.872098 -70 AAAACGCCATTTTTTTAGATAATTAAGGCAAA 4 16 0 TTTTTTGATA 0.93956 -58 GCGTTTTTCCCTTTTTGAATCAATTTAGATGA 4 41 1 CTTTTTAATA 0.821344 -33 AAAGGTGTGCTTTTTTAATTGATACAGTTAAT 5 25 1 TTTTTTATTA 0.890069 -276 TAAGCTTAATTTTTTTAACTGAACCGCTCATG 7 18 1 TTTTTTACTA 0.947991 -167 ATTTTATCCCTTTTTTATAACAGATTACACTA 8 12 1 TTTTTTTAAA 0.843081 -51 TTTAAGATTGTTTTTTTAATTAGTGTAATCTG 8 32 0 TTTTTTAATA 0.966751 -31 TGCTAAAGCCTTTTTTAAATCACCGATTAAAG 9 34 0 TTTTTTAATA 0.96343 -210 AAGATCACTATTTTTTTTCTCAAAGAGCTTAA 9 162 1 TTTTTTTCTA 0.938887 -82 ****** *** * Masking position 12 Map Score: 14.5468 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 46 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 CAGGTAAATAATTCAAAAAACACAGGCGTT 3 192 0 ATTCAAAAAA 0.878544 -109 AAACGTAGTCAAATAAAAAAGTTTGGCGCT 3 233 1 AAATAAAAAA 0.749631 -68 TGCCTTAATTATCTAAAAAAATGGCGTTTT 4 18 1 ATCTAAAAAA 0.846322 -56 ATCTAAATTGATTCAAAAAGGGAAAAACGC 4 41 0 ATTCAAAAAG 0.827477 -33 TAACTGTATCAATTAAAAAAGCACACCTTT 5 25 0 AATTAAAAAA 0.95929 -276 TGAGCGGTTCAGTTAAAAAAATTAAGCTTA 7 18 0 AGTTAAAAAA 0.830918 -167 AGATTACACTAATTAAAAAAACAATCTTAA 8 33 1 AATTAAAAAA 0.95929 -30 TTAATCGGTGATTTAAAAAAGGCTTTAGCA 9 36 1 ATTTAAAAAA 0.916026 -208 TTTTAGTTAGAATTAAACAATTTAAGCTCT 9 185 0 AATTAAACAA 0.774644 -59 GTTTAATTCTAACTAAAATAATCCTGATAG 9 197 1 AACTAAAATA 0.690621 -47 TTGCTAACAAAATCAAAATAAGTTATCAGA 10 71 0 AATCAAAATA 0.74568 -230 ATCTAAAGCAAACCAAAAAGTCACCTGTTT 10 117 1 AACCAAAAAG 0.839493 -184 GCAGTTCCACAATTAAAAAGCCACCCGTTA 10 148 0 AATTAAAAAG 0.939849 -153 CATAATGTAAAATTACAAAGC 10 290 1 AATTACAAAG 0.695054 -11 ********** Masking position 5 Map Score: 11.6979 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 162 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 AGTCAAGGGGTGAACCCCACAAAATCAGCCCCCAAACTTAT 1 84 0 TAACCCGCCC 0.964314 -74 TGCGTGGGTTCGAATCCCACAGTCTCCGCCAAAATATTAAC 5 51 0 CAACCCGCCA 0.997817 -250 TAACGCTTTTCGAGAGCGCCCCCTTAAACCACTTGGGTAAG 5 104 1 CAGGCCACCA 0.935193 -197 TGCGAGGGTTCGAATCCCTCAGTATCCGCCACGGAGACTTA 5 141 0 CAACCCGCCA 0.997817 -160 TATAAGCTTTCCAAGCCTACCCCTTCAGCCACTTGGGTAAG 5 196 1 CAACCCGCCA 0.997817 -105 TTGAGGGGCGCTAAACCTTTCCTTAAAGCCAACTAGAATAA 7 116 1 CAACCTGCCA 0.985996 -69 AAATCACCGATTAAAGCATCTAATCAAGCACGTTTAGCA 9 9 0 TAAGCCGCAC 0.738077 -235 CATTAAAGCACAAAAGCTTTACTTTGTACCAACTGCTAAAG 9 58 0 CAAGCTACCA 0.921907 -186 ATCTACATTGCTAAGCGTGCTGTACAAGCCATTAAAGCACA 9 87 0 CAACGCGCCA 0.981608 -157 TGGAGGGGATCAAATGCACCACCAAAGATCACTATTTTTTT 9 138 1 CAAGCCATCA 0.857909 -106 GCAATAACACCAAAATCCACATCTAAAGCAAACCAAAAAGT 10 97 1 CAATCCGCAA 0.901307 -204 * ** ** * **** Masking position 3 Map Score: 10.1925 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 66 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 AGGGGTGAACCCCACAAAATCAGCCCCCAAACTTA 1 85 0 CCACTCAGCC 0.995917 -73 GGGTTCGAATCCCACAGTCTCCGCCAAAATATTAA 5 52 0 CCACTCCGCC 0.991683 -249 GGGTTCGAATCCCTCAGTATCCGCCACGGAGACTT 5 142 0 CCTCTCCGCC 0.974145 -159 GCTTTCCAAGCCTACCCCTTCAGCCACTTGGGTAA 5 201 1 CCACTCAGCC 0.995917 -100 GGGCGCTAAACCTTTCCTTAAAGCCAACTAGAATA 7 121 1 CCTTAAAGCC 0.89677 -64 TTACTTTGTACCAACTGCTAAAGCCTTTTTTAAAT 9 46 0 CCACAAAGCC 0.990174 -198 TAAAATAATCCTGATAGCTACAGCCATTTGTGCTG 9 210 1 CTATACAGCC 0.857779 -34 CTTGCAGTTCCACAATTAAAAAGCCACCCGTTAAA 10 146 0 CAAAAAAGCC 0.754289 -155 CATTTTTGTGCCAAAGTGTTAAGCCAAACATTGTC 10 209 0 CCAATAAGCC 0.971321 -92 ** ** ****** Masking position 14 Map Score: 7.71235 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 17 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TAGTTATTAGTAATTAATTAGTTAACAGCC 1 23 1 TAATTAATTA 0.481932 -135 GTAATTGGTGTAAGTAATGATAAGACCTTA 3 123 1 TAAGTAATGA 0.91819 -178 AACACAGGCGTTAATAATGATGATTGAAGC 3 174 0 TTAATAATGA 0.701399 -127 TTTTTTTAGATAATTAAGGCAAATTTTT 4 9 0 TAATTAAGGC 0.908316 -65 AGCTCTTAATTAAGGAAGTTAAGCTG 6 7 1 TAATTAAGGA 0.970302 -82 AGTTAGATTGTAAGTAAGTATTACAAGTAC 7 52 1 TAAGTAAGTA 0.821927 -133 TTAATAAGAATTATTAAGGAGCTTGCAGTT 10 172 0 TTATTAAGGA 0.956187 -129 TTAATAATTCTTATTAAGGAGGATGACAAT 10 185 1 TTATTAAGGA 0.956187 -116 CAAGTTAACTTAATTAATGATTGCTAACCA 10 248 0 TAATTAATGA 0.81575 -53 ********** Masking position 5 Map Score: 8.37829 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 70 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TCACCCCTTGACTGGGCTAATTTCTTATTTTG 1 112 1 ACTGGGAATT 0.979452 -46 GAATTAATACTTGTTGAATTATAACAAAAT 1 138 0 ACTTGTAATT 0.898826 -20 CTCTTCCCTCATGGGGGTAATTGGTGTAAGTA 3 107 1 ATGGGGAATT 0.889043 -194 CCCTTAAACCACTTGGGTAAGTCTCCGTGGCG 5 124 1 ACTTGGAAGT 0.946364 -177 CCCTTCAGCCACTTGGGTAAGTATCCCCTTTC 5 216 1 ACTTGGAAGT 0.946364 -85 GATAAGTCAACTGGGTCAATTTTAATTTGTA 5 280 0 ACTGGGAATT 0.978303 -21 GTTAAGCTGTAAGTGGGGAATTAAAGCTTTGA 6 28 1 AAGTGGAATT 0.861365 -61 AGAGTTAAATATTGGGAAAATTTTAACTTTTC 6 58 0 ATTGGGAATT 0.942433 -31 AAAGAGCTTAAATTGTTTAATTCTAACTAAAA 9 183 1 AATTGTAATT 0.709977 -61 ****** **** Masking position 9 Map Score: 7.87171 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 41 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 CCAAAACAACCACCTTAAGTGGGCTGTTAACTAAT 1 39 0 CCCTGTGGGT 0.995162 -119 AGTTTGGGGGCTGATTTTGTGGGGTTCACCCCTTG 1 87 1 CGATGTGGGT 0.992392 -71 GTGGGGTTCACCCCTTGACTGGGCTAATTTCTTAT 1 105 1 CCCTCTGGGT 0.971453 -53 AAAGCACATCCCCAAAAGGTGTGCTTTTTTAATTG 5 11 1 CCAAGTGTGT 0.90079 -290 AATATTTTGGCGGAGACTGTGGGATTCGAACCCAC 5 54 1 CGAAGTGGGT 0.987844 -247 TTAGGTGTTTTTGCATGCGTGGGTTCGAATCCCAC 5 72 0 TGCTGTGGGT 0.958511 -229 GTCTCCGTGGCGGATACTGAGGGATTCGAACCCTC 5 144 1 CGAAGAGGGT 0.967486 -157 AGATGGGTAACACCATGCGAGGGTTCGAATCCCTC 5 162 0 CCCTGAGGGT 0.986687 -139 * ** * ***** * Masking position 15 Map Score: 6.45562 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 24 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 GATAGTTATTAGTAATTAATTAGTTAACAGC 1 21 1 AGAATTAATT 0.631235 -137 GGATGACCCTAGTACTAAAATCAATAAGACT 2 20 1 AGACTAAAAT 0.895747 -26 GACAGTTATTAGAGAAAAAATGAGGAC 3 7 0 AGGAAAAAAT 0.927151 -294 ACTGTCAATGAGTGCTAAAACTTCATATATT 3 32 1 AGGCTAAAAC 0.863956 -269 CCATGAGGGAAGAGATAAAGTAGAGAATAAT 3 90 0 AGGATAAAGT 0.881872 -211 TTTAGATAGGAGCGAATAAATGTGTA 3 285 1 AGGAATAAAT 0.896833 -16 TTAATTTGTAAGCGCTTAATTGCTAATAAAT 5 259 0 AGGCTTAATT 0.867948 -42 GTTATAAAAAAGGGATAAAATG 8 2 0 AGGATAAAAT 0.965644 -61 AAGCTCTTTGAGAAAAAAAATAGTGATCTTT 9 161 0 AGAAAAAAAT 0.782183 -83 TTTTTCTCAAAGAGCTTAAATTGTTTAATTC 9 175 1 AGGCTTAAAT 0.954128 -69 ** ******** Masking position 8 Map Score: 5.46793 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 68 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 GGATTCGAACCCACGCATGCAAAAACACCTAA 5 75 1 CCGCATGCAA 0.750312 -226 CGAGAGCGCCCCCTTAAACCACTTGGGTAAGT 5 114 1 CCTAAACCAC 0.969787 -187 CCAAGCCTACCCCTTCAGCCACTTGGGTAAGT 5 206 1 CCTCAGCCAC 0.90231 -95 CTAGAATAATCTAGTAATGCACTATTGCAAAA 7 148 1 CTTAATGCAC 0.882252 -37 ATTAAAGCATCTAATCAAGCACGTTTAGCA 9 9 0 CTTCAAGCAC 0.962531 -235 GCTGTACAAGCCATTAAAGCACAAAAGCTTTA 9 78 0 CCTAAAGCAC 0.986366 -166 GCTTTAATGGCTTGTACAGCACGCTTAGCAAT 9 90 1 CTTACAGCAC 0.944078 -154 TGCATTTGATCCCCTCCACCAAGCGCATATCT 9 124 0 CCTCCACCAA 0.874784 -120 GGACCTGGACAGCACAAATGGCTGT 9 229 0 CCGACAGCAC 0.956801 -15 CCAAAATCCACATCTAAAGCAAACCAAAAAGT 10 106 1 CATAAAGCAA 0.725859 -195 ** ******** Masking position 11 Map Score: 4.35127 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 91 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TAGTTAACAGCCCACTTAAGGTGGTTGTTT 1 41 1 CCCACTTAAG 0.936876 -117 TGTGGGGTTCACCCCTTGACTGGGCTAATT 1 104 1 ACCCCTTGAC 0.986538 -54 ACACCAATTACCCCCATGAGGGAAGAGATA 3 104 0 CCCCCATGAG 0.918853 -197 TTCGAGAGCGCCCCCTTAAACCACTTGGGT 5 112 1 CCCCCTTAAA 0.952606 -189 TTCCAAGCCTACCCCTTCAGCCACTTGGGT 5 204 1 ACCCCTTCAG 0.940639 -97 TTAAAATTGACCCAGTTGACTTATC 5 286 1 CCCAGTTGAC 0.904014 -15 AGTTGCACCAACCACTTGTCTTTGGCAAAC 7 84 0 ACCACTTGTC 0.791069 -101 AGTCCTAAAAATCCCTTAACACAACCTATG 10 26 0 ATCCCTTAAC 0.819151 -275 TTAAAAAGCCACCCGTTAAAAACAGGTGAC 10 136 0 ACCCGTTAAA 0.826246 -165 ********** Masking position 7 Map Score: 2.58578 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 67 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 AATAAAAAAGTTTGGCGCTTTAAATTCTCC 3 244 1 TTTGGCGCTT 0.931896 -57 AAGACAAGTGGTTGGTGCAACTAGTTGAGG 7 92 1 GTTGGTGCAA 0.974357 -93 GGCTTTAGCAGTTGGTACAAAGTAAAGCTT 9 56 1 GTTGGTACAA 0.896808 -188 AAAGTAAAGCTTTTGTGCTTTAATGGCTTG 9 74 1 TTTTGTGCTT 0.729613 -170 AGTGATCTTTGGTGGTGCATTTGATCCCCT 9 141 0 GGTGGTGCAT 0.909846 -103 AGATGTGGATTTTGGTGTTATTGCTAACAA 10 91 0 TTTGGTGTTA 0.729613 -210 GGCTTAACACTTTGGCACAAAAATGGTGTT 10 219 1 TTTGGCACAA 0.833848 -82 ACTTGCTCTGTTTGGTGCATAATGTAAAAT 10 273 1 TTTGGTGCAT 0.974852 -28 ********** Masking position 3 Map Score: 2.6537 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 152 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TATTGATTTTAGTACTAGGGTCATCCCAGTA 2 15 0 AGTACTAGGT 0.978865 -31 TTGTCTTTTTTGTACTAGCTTCAATCATCAT 3 157 1 TGTACTAGTT 0.968991 -144 AAGTATTACAAGTACTAGTTTGCCAAAGACA 7 67 1 AGTACTAGTT 0.990367 -118 GCAATAGTGCATTACTAGATTATTCTAGTTG 7 145 0 ATTACTAGTT 0.951693 -40 AGTACTAGGTTTAAGATTGTT 8 52 0 AGTACTAGTT 0.990367 -11 ******** ** Masking position 6 Map Score: 4.91565 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 TGAATTATAACAAAATAAGAAATTAGCCCAG 1 123 0 CAAAATAGAA 0.978847 -35 ACAGCAGCCACAATATATGAAGTTTTAGCAC 3 43 0 CAATATAGAA 0.905724 -258 TTTACCTGTTCAAAAAAAGAAACGTAGTCAA 3 214 1 CAAAAAAGAA 0.952677 -87 TAAATTGATTCAAAAAGGGAAAAACGCCATT 4 37 0 CAAAAAGGAA 0.861002 -37 CAGTCTCCGCCAAAATATTAACTGTATCAAT 5 42 0 CAAAATATAA 0.857192 -259 CAACCTATGTCTAAATATGAAAAA 10 4 0 CTAAATAGAA 0.952676 -297 TGTCATCCTCCTTAATAAGAATTATTAAGGA 10 182 0 CTTAATAGAA 0.806927 -119 ******* *** Masking position 5 Map Score: 2.82687 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 38 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 TAACTAATTAATTACTAATAACTATCAAAGT 1 16 0 ATTACTAAAA 0.88874 -142 ACTGTCAATGAGTGCTAAAACTTCATATATT 3 32 1 AGTGCTAAAC 0.927031 -269 TAAGCGCTTAATTGCTAATAAATGCAAAATT 5 251 0 ATTGCTAAAA 0.981001 -50 GCATATCTACATTGCTAAGCGTGCTGTACAA 9 101 0 ATTGCTAACG 0.927031 -143 TTACATGGATAGTCCTAAAAATCCCTTAACA 10 35 0 AGTCCTAAAA 0.888476 -266 TTTTGGTGTTATTGCTAACAAAATCAAAATA 10 81 0 ATTGCTAAAA 0.981001 -220 TTAATTAATGATTGCTAACCAACACCATTTT 10 238 0 ATTGCTAACA 0.972024 -63 ******** ** Masking position 7 Map Score: 3.49222 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 49 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 ********** No masking Map Score: 5.70866e-13 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