AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -isoxS_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 araD 300 L-ribulose-5-phosphate 4-epimerase; similar to Swiss-Prot Accession Number P08203, from E. coli #2 rpl21 146 ribosomal protein L21; similar to Swiss-Prot Accession Number P26908, from B. subtilis #3 nrdE 23 ribonucleoside-diphosphate reductase; similar to Swiss-Prot Accession Number Q08698, from S. typhimurium #4 thyA 300 thymidylate synthase; similar to Swiss-Prot Accession Number P13954, from S. aureus Motif number 1 TTATCGAATGAAGCTGCTATTAAAGAGTGTTT 1 38 0 AACTGCTTTA 0.965772 -263 ATGTCCCCTAAAACTGTTCTTACAAATCTTTT 1 161 1 AACTGTTTTA 0.978285 -140 AGCAGGGGTTAATTTGTTATAATTTCACGCTT 2 58 1 AATTGTTTAA 0.698862 -89 ATACCAAAAGAAACGGTTTTATTGAAA 2 130 1 AACGGTTTAT 0.977122 -17 TAACTATTCAAACCGGTGGTTAAGAGATAAAC 4 45 0 AACGGTGTTA 0.971632 -256 TGAGCTGCTAAAACGGCTTTTTAGTGTCTTAT 4 79 1 AACGGCTTTT 0.975746 -222 AAGGCTTTCTAAGCGCTTATAAGACACTAAAA 4 97 0 AACGCTTTAA 0.962342 -204 GGGGGCTTACAAGCGGTTATTAACATTGTTTT 4 181 1 AACGGTTTTA 0.994532 -120 ACATTGTTTTAACAGGTTATTAACATTGTTTT 4 203 1 AAAGGTTTTA 0.940794 -98 ATAAGCTTTAAAGCGGTTTTAACACTGCAAAA 4 255 0 AACGGTTTAA 0.990761 -46 TTAAACGCCTTTTTTTAAAGCTTT 4 287 0 AACGCCTTTT 0.915195 -14 ** ***** *** Masking position 2 Map Score: 17.5846 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 143 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 ATCGAATGAAGCTGCTATTAAAGAGTGTTT 1 38 0 GCTGCTATTA 0.876844 -263 TGACTGTCACGATCATTTAATTAAGAATTG 1 107 0 GATCATTTAA 0.488379 -194 TTATAATTTCACGCTTATTTGCGTCTTCTG 2 74 1 ACGCTTATTT 0.876656 -73 ACCAAAAGAAACGGTTTTATTGAAA 2 132 1 ACGGTTTTAT 0.843058 -15 ATAAACGCTGAATGCTTTTTGTATTTTTTG 4 21 0 AATGCTTTTT 0.537109 -280 AGCTGCTAAAACGGCTTTTTAGTGTCTTAT 4 81 1 ACGGCTTTTT 0.926682 -220 GGCTTTCTAAGCGCTTATAAGACACTAAAA 4 97 0 GCGCTTATAA 0.918735 -204 GGCCTGTAGGGCTCATTTTAGGCTCAAGCT 4 146 0 GCTCATTTTA 0.865881 -155 GGGCTTACAAGCGGTTATTAACATTGTTTT 4 183 1 GCGGTTATTA 0.937427 -118 TGAGCTAATGGAGCCTTTTAAAACAATGTT 4 224 0 GAGCCTTTTA 0.923608 -77 GGCTCCATTAGCTCATTTTTGCAGTGTTAA 4 239 1 GCTCATTTTT 0.830574 -62 AAGCTTTAAAGCGGTTTTAACACTGCAAAA 4 255 0 GCGGTTTTAA 0.937427 -46 AACCGCTTTAAAGCTTATAAAGCTTTAAAA 4 269 1 AAGCTTATAA 0.580529 -32 TTAAACGCCTTTTTTTAAAGCTTT 4 287 0 ACGCCTTTTT 0.943576 -14 ********** Masking position 6 Map Score: 9.50564 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 621 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 3 ACCCTAAGGATTTAGGTATTTGTGACTGTC 1 129 0 TTTAGGTATT 0.939114 -172 TTAAATGGTTTAAGTGTATTGAAATAACCC 1 209 1 TAAGTGTATT 0.845071 -92 TATATGTATTTATATGTATTA 2 2 0 TATATGTATT 0.934508 -145 CTAGACTTACTATATGTATTTATATGTATT 2 12 0 TATATGTATT 0.934508 -135 TTCACGCTTATTTGCGTCTTCTGCGGTTCC 2 81 1 TTTGCGTCTT 0.928751 -66 AAACCGTTTCTTTTGGTATTTTGTATAAAC 2 119 0 TTTTGGTATT 0.892124 -28 CTTTTTGTATTTTTTGTCTTATGGCA 4 7 0 TTTTTGTCTT 0.9495 -294 GCATTCAGCGTTTATCTCTTAACCACCGGT 4 36 1 TTTATCTCTT 0.835992 -265 AAACGGCTTTTTAGTGTCTTATAAGCGCTT 4 89 1 TTAGTGTCTT 0.930494 -212 ********** Masking position 7 Map Score: 6.60522 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 126 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TTTAGAAATGAAAAGATTTGTAAGAACAGTTTT 1 170 0 AAAAGATTAA 0.862603 -131 TCAATACACTTAAACCATTTAACGTCCATTTAG 1 198 0 TAAACCTAAC 0.693644 -103 GTGTATTGAAATAACCCTAATAATGTGTAAGCT 1 222 1 ATAACCTTAA 0.91918 -79 TAATTTGCCATTAACAGTTGTAAAGCTGGCAAC 1 261 1 TTAACATTAA 0.833732 -40 TATAACAAATTAACCCCTGCTAAAGTCATGCTT 2 46 0 TAACCCTTAA 0.953727 -101 AATTGGCTAATCATTAATAACGG 3 4 0 TAATCATTAA 0.874397 -20 ACAATGTTAATAACCGCTTGTAAGCCCCCAAAA 4 177 0 TAACCGTTAA 0.855337 -124 ATAACCTGTTAAAACAATGTTAATAACCGCTTG 4 190 0 AAAACATTAA 0.94973 -111 GGAGCCTTTTAAAACAATGTTAATAACCTGTTA 4 212 0 AAAACATTAA 0.94973 -89 TAAAGCGGTTTTAACACTGCAAAAATGAGCTAA 4 246 0 TTAACATAAA 0.801231 -55 CGCCTTTTTTTAAAGCTTTATAAGCTTTAAAGC 4 273 0 TAAAGCTTAA 0.920261 -28 ****** * *** Masking position 3 Map Score: 6.0379 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 166 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 CTTTGGCTTCCGGACCCCAATTCTTAATTA 1 90 1 CGGACCCCAA 0.979922 -211 TTAGGGGACATTGACCCTAAGGATTTAGGT 1 142 0 TTGACCCTAA 0.978 -159 GGCTGATTCTAAAAATAGTTGC 1 289 0 CTGATTCTAA 0.92557 -12 GCGTCTTCTGCGGTTCCTAAATTTTGTTTA 2 94 1 CGGTTCCTAA 0.955142 -53 TTTTCCTAGCTTGAGCCTAAAATGAGCCCT 4 139 1 TTGAGCCTAA 0.959324 -162 ********** Masking position 9 Map Score: 0.139834 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 = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 ********** No masking Map Score: -9.70439e-14 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 7 ********** No masking Map Score: -9.70439e-14 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 8 ********** No masking Map Score: -9.70439e-14 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