AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -ilexA_mpneu_opreg_300.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 CCAAACTTATAATAAATAAACCAAAACAACCACCTTAAG 1 55 0 AAATAACAAA 0.951822 -103 ATAACAAAATAAGAAATTAGCCCAGTCAAGGGGTGAACC 1 109 0 AAATTACAAA 0.974593 -49 TACCTGTTCAAAAAAAGAAACGTAGTCAAATAAAAAAGT 3 216 1 AAAGAACAAA 0.728301 -85 AGTCAAATAAAAAAGTTTGGCGCTTTAAATTCTCCTTAC 3 239 1 AAATTGCTAA 0.89833 -62 AAAAATTTGCCTTAATTATCTAAAAAAAT 4 1 1 AAATTGCAAT 0.861743 -73 AGTCTCCGCCAAAATATTAACTGTATCAATTAAAAAAGC 5 33 0 AAATTACTAA 0.935971 -268 TGCATTTATTAGCAATTAAGCGCTTACAAATTAAAATTG 5 256 1 AGATAACTAA 0.68606 -45 AAATATTGGGAAAATTTTAACTTTTCAAAGCTTTAATTC 6 45 0 AAATTACTAA 0.935971 -44 GTTCAGTTAAAAAAATTAAGCTTAATTAAGT 7 3 0 AAATAACAAA 0.951822 -182 TATTACAAGTACTAGTTTGCCAAAGACAAGTGGTTGGTG 7 70 1 ACATTGCAAA 0.78527 -115 GCACTATTGCAAAATCTAACCTGATTTAA 7 166 1 AAATAACAAA 0.951822 -19 CCTTTTTTATAACAGATTACACTAATTAAAAAAACAATC 8 20 1 AAATTAAAAA 0.684589 -43 ACAAAATCAAAATAAGTTATCAGATGTATTTACATGGAT 10 56 0 AAATTACAAT 0.911617 -245 TGTTTGGCTTAACACTTTGGCACAAAAATGGTGTTGGTT 10 214 1 AAATTGCAAT 0.861766 -87 CACCAAACAGAGCAAGTTAACTTAATTAATGATTGCTAA 10 251 0 AGATTACAAA 0.917589 -50 ** * *** * * ** Masking position 4 Map Score: 13.7929 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 91 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 AAATAAACCAAAACAACCACCTTAAGTGGGCTGTTAA 1 44 0 AACACATAGT 0.781563 -114 TCAAGGGGTGAACCCCACAAAATCAGCCCCCAAACTT 1 86 0 AACCCATAGC 0.994575 -72 CGTGGGTTCGAATCCCACAGTCTCCGCCAAAATATTA 5 53 0 AACCCATCGC 0.985986 -248 CGAGGGTTCGAATCCCTCAGTATCCGCCACGGAGACT 5 143 0 AACCCATCGC 0.985986 -158 TAAGCTTTCCAAGCCTACCCCTTCAGCCACTTGGGTA 5 198 1 AACCCCTAGC 0.987473 -103 TCAAAGCTTTAATTCCCCACTTACAGCTTAACTTCCT 6 23 0 AATCCAAAGC 0.975437 -66 GAGGGGCGCTAAACCTTTCCTTAAAGCCAACTAGAAT 7 118 1 AACCTCAAGC 0.785497 -67 TAAAGCATCTAATCAAGCACGTTTAGCA 9 2 0 AACACATAGC 0.978453 -242 AGCCTTTTTTAAATCACCGATTAAAGCATCTAATCAA 9 23 0 AATCCGAAGC 0.902707 -221 TTTTAGTTAGAATTAAACAATTTAAGCTCTTTGAGAA 9 178 0 AATACATAGC 0.94345 -66 AATAACACCAAAATCCACATCTAAAGCAAACCAAAAA 10 99 1 AATCCAAAGC 0.975437 -202 ** ** ** * *** Masking position 2 Map Score: 12.2749 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 66 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 TAGTTATTAGTAATTAATTAGTTAACAGCC 1 23 1 TAATTAATTA 0.486252 -135 TTGACTGGGCTAATTTCTTATTTTGTTATA 1 119 1 TAATTTCTTA 0.533426 -39 TAAGGTCTTATCATTACTTACACCAATTAC 3 123 0 TCATTACTTA 0.922475 -178 GCTTCAATCATCATTATTAACGCCTGTGTT 3 174 1 TCATTATTAA 0.71767 -127 TGTGTTTTTTGAATTATTTACCTGTTCAAA 3 198 1 GAATTATTTA 0.624148 -103 AAAAATTTGCCTTAATTATCTAAAAAAA 4 9 1 GCCTTAATTA 0.946604 -65 CTATAATTTTGCATTTATTAGCAATTAAGC 5 247 1 GCATTTATTA 0.804846 -54 CAGCTTAACTTCCTTAATTAAGAGCT 6 7 0 TCCTTAATTA 0.956927 -82 GTACTTGTAATACTTACTTACAATCTAACT 7 52 0 TACTTACTTA 0.82964 -133 AACTGCTAAAGCCTTTTTTAAATCACCGAT 9 39 0 GCCTTTTTTA 0.720759 -205 AACTGCAAGCTCCTTAATAATTCTTATTAA 10 172 1 TCCTTAATAA 0.885659 -129 ATTGTCATCCTCCTTAATAAGAATTATTAA 10 185 0 TCCTTAATAA 0.885659 -116 TGGTTAGCAATCATTAATTAAGTTAACTTG 10 248 1 TCATTAATTA 0.836821 -53 ********** Masking position 10 Map Score: 9.80617 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 187 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 TAAACCAAAACAACCACCTTAAGTGGGCTG 1 48 0 CAACCACCTT 0.84345 -110 GCGCCCCCTTAAACCACTTGGGTAAGTCTC 5 119 1 AAACCACTTG 0.950193 -182 CCTACCCCTTCAGCCACTTGGGTAAGTATC 5 211 1 CAGCCACTTG 0.986806 -90 GATAAGTCAACTGGGTCAATTTT 5 288 0 AAGTCAACTG 0.836999 -13 CTAGTTGCACCAACCACTTGTCTTTGGCAA 7 86 0 CAACCACTTG 0.960866 -99 CCTTTCCTTAAAGCCAACTAGAATAATCTA 7 131 1 AAGCCAACTA 0.74497 -54 CTGATAGCTACAGCCATTTGTGCTGTCCAG 9 220 1 CAGCCATTTG 0.9067 -24 GCAAACCAAAAAGTCACCTGTTTTTAACGG 10 124 1 AAGTCACCTG 0.957419 -177 CACAATTAAAAAGCCACCCGTTAAAAACAG 10 141 0 AAGCCACCCG 0.963927 -160 ********** Masking position 6 Map Score: 7.06254 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 60 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 AAAACAACCACCTTAAGTGGGCTGTTAACTAATTA 1 37 0 CCTTAAGGTT 0.784164 -121 CTAAATGAATGTGTAAGGAGAATTTAAAGCGCCAA 3 255 0 GTGTAAGGTT 0.828374 -46 CTCTCGAAAAGCGTTAGGTGTTTTTGCATGCGTGG 5 85 0 GCGTTAGGTT 0.97063 -216 TACCCAAGTGGTTTAAGGGGGCGCTCTCGAAAAGC 5 108 0 GTTTAAGGGT 0.91183 -193 ATTCTAGTTGGCTTTAAGGAAAGGTTTAGCGCCCC 7 120 0 GCTTTAAAGT 0.745772 -65 TTGATTAGATGCTTTAATCGGTGATTTAAAAAAGG 9 23 1 GCTTTAAGGT 0.973843 -221 TTTAAAAAAGGCTTTAGCAGTTGGTACAAAGTAAA 9 47 1 GCTTTAGGGT 0.986074 -197 AAGCTTTTGTGCTTTAATGGCTTGTACAGCACGCT 9 80 1 GCTTTAAGTT 0.965208 -164 TTCTCAAAGAGCTTAAATTGTTTAATTCTAACTAA 9 178 1 GCTTAAAGTA 0.675151 -66 GACATAGGTTGTGTTAAGGGATTTTTAGGACTATC 10 24 1 GTGTTAAGTT 0.811466 -277 TTTTTGGTTTGCTTTAGATGTGGATTTTGGTGTTA 10 101 0 GCTTTAGGGT 0.986074 -200 ******* * * * Masking position 6 Map Score: 6.14834 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 157 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 AACAGGTAAATAATTCAAAAAACACAGGCG 3 194 0 TAATTCAAAA 0.758275 -107 AATTATTTACCTGTTCAAAAAAAGAAACGT 3 209 1 CTGTTCAAAA 0.70192 -92 GAAACGTAGTCAAATAAAAAAGTTTGGCGC 3 232 1 CAAATAAAAA 0.898889 -69 TTAACTGTATCAATTAAAAAAGCACACCTT 5 26 0 CAATTAAAAA 0.965673 -275 TAAGCGCTTACAAATTAAAATTGACCCAGT 5 272 1 CAAATTAAAA 0.648586 -29 ATGAGCGGTTCAGTTAAAAAAATTAAGCTT 7 19 0 CAGTTAAAAA 0.958684 -166 CAGATTACACTAATTAAAAAAACAATCTTA 8 32 1 TAATTAAAAA 0.847042 -31 AAAAAGCCACCCGTTAAAAACAGGTGACTT 10 134 0 CCGTTAAAAA 0.860399 -167 TGCAGTTCCACAATTAAAAAGCCACCCGTT 10 149 0 CAATTAAAAA 0.965673 -152 ********** Masking position 5 Map Score: 5.78146 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 88 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 CCACAAAATCAGCCCCCAAACTTATAATAA 1 79 0 AGCCCCCAAA 0.90876 -79 AAGGGGTGAACCCCACAAAATCAGCCCCCA 1 91 0 CCCCACAAAA 0.861982 -67 GGAGAATTTAAAGCGCCAAACTTTTTTATT 3 244 0 AAGCGCCAAA 0.897442 -57 AAAGCACATCCCCAAAAGGTGTGCTTT 5 8 1 ATCCCCAAAA 0.878733 -293 ATCCCACAGTCTCCGCCAAAATATTAACTG 5 49 0 CTCCGCCAAA 0.966061 -252 CAAGCCATTAAAGCACAAAAGCTTTACTTT 9 74 0 AAGCACAAAA 0.809956 -170 ATTTGATCCCCTCCACCAAGCGCATATCTA 9 123 0 CTCCACCAAG 0.908117 -121 GGATCAAATGCACCACCAAAGATCACTATT 9 144 1 CACCACCAAA 0.970137 -100 ATTTTACATTATGCACCAAACAGAGCAAGT 10 273 0 ATGCACCAAA 0.944236 -28 ********** Masking position 8 Map Score: 4.24727 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 125 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 GTCCTCATTTTTTCTCTAATAACTGTCA 3 9 1 TTTTTCTCTA 0.954708 -292 GCTGTAGGTATTATTCTCTACTTTATCTCT 3 81 1 TTATTCTCTA 0.813992 -220 TATTCTCTACTTTATCTCTTCCCTCATGGG 3 92 1 TTTATCTCTT 0.954708 -209 AAAAATGGCGTTTTTCCCTTTTTGAATCAA 4 34 1 TTTTTCCCTT 0.948637 -40 TTTCCCAATATTTAACTCTTCTCTAGCA 6 71 1 TTTAACTCTT 0.813992 -18 CATTTTATCCCTTTTTTATAACA 8 4 1 TTTATCCCTT 0.934142 -59 ATCACTATTTTTTTTCTCAAAGAGCTTAAA 9 165 1 TTTTTCTCAA 0.813992 -79 ********** Masking position 2 Map Score: 3.1985 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 22 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 9 CTGTGGGATTCGAACCCACGCATGCAAAAA 5 70 1 CGAACCCACG 0.990261 -231 GCCACGGAGACTTACCCAAGTGGTTTAAGG 5 125 0 CTTACCCAAG 0.977364 -176 CTGAGGGATTCGAACCCTCGCATGGTGTTA 5 160 1 CGAACCCTCG 0.976157 -141 AAAGGGGATACTTACCCAAGTGGCTGAAGG 5 217 0 CTTACCCAAG 0.977364 -84 ********** Masking position 4 Map Score: 1.2424 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 1 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 10 TAACTAATTAATTACTAATAACTATCAAAG 1 17 0 ATTACTAATA 0.812902 -141 GGATGACCCTAGTACTAAAATCAATAAGAC 2 20 1 AGTACTAAAA 0.897778 -26 ACTGTCAATGAGTGCTAAAACTTCATATAT 3 32 1 AGTGCTAAAA 0.945222 -269 GATTGAAGCTAGTACAAAAAAGACAATGAT 3 153 0 AGTACAAAAA 0.70942 -148 TAAGCGCTTAATTGCTAATAAATGCAAAAT 5 252 0 ATTGCTAATA 0.895137 -49 GCATATCTACATTGCTAAGCGTGCTGTACA 9 102 0 ATTGCTAAGC 0.903858 -142 TTACATGGATAGTCCTAAAAATCCCTTAAC 10 36 0 AGTCCTAAAA 0.798242 -265 TTTTGGTGTTATTGCTAACAAAATCAAAAT 10 82 0 ATTGCTAACA 0.929597 -219 TTAATTAATGATTGCTAACCAACACCATTT 10 239 0 ATTGCTAACC 0.903858 -62 ATAATGTAAAATTACAAAGC 10 291 1 ATTACAAAGC 0.570843 -10 ********** Masking position 7 Map Score: 4.39376 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 100 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 TCGAATCCCACAGTCTCCGCCAAAATATTA 5 53 0 CAGTCTCCGC 0.992984 -248 CCACTTGGGTAAGTCTCCGTGGCGGATACT 5 132 1 AAGTCTCCGT 0.958373 -169 TCGAATCCCTCAGTATCCGCCACGGAGACT 5 143 0 CAGTATCCGC 0.989183 -158 CCACTTGGGTAAGTATCCCCTTTCTATAAT 5 224 1 AAGTATCCCC 0.956623 -77 ********** Masking position 6 Map Score: 0.904381 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 1 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 ********** 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 Motif number 13 ********** 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 Motif number 14 ********** 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