AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_mpneu_reg_100.orf -o00130_mpneu_100.ace -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/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 D12_orf212 101 dnaE; [EC:2.7.7.-] [SP:PRIM_MYCPN] #2 K05_orf425 300 hypothetical protein. #3 F11_orf339 300 lplA; probable lipoate-protein ligase A. [EC:6.-.-.-] #4 H91_orf620 52 dnaG, dnaE; DNA primase. [EC:2.7.7.-] [SP:PRIM_MYCPN] #5 H91_orf164 300 hypothetical protein. Motif number 1 GTAAGCGCCAAAATAAAAATACCAACAGATAACCT 1 50 0 AAAAAATAAA 0.966285 -52 GTTTTATTATAAAAGAAATAACTAACCTTCGGAGT 2 31 1 AAAAAAAAAA 0.876715 -270 CTGTCTACTGCAATCTAGTTATAAAAAACTCACCT 2 115 1 CAATAGTAAA 0.800682 -186 AACTCACCTAAAAGGTAGTTATTAACACCAAAAAA 2 141 1 AAATAGTAAA 0.95522 -160 GAGTTTATTTAATTGAAACTAAGAACGCTTCTAAA 2 180 0 AATAAATAAA 0.801304 -121 CTTGAAGATAACGTTTAAGTATCAACTTCATGGTT 2 255 1 ACGTAATAAA 0.816467 -46 AAGATTGCTAACACAAAACTAGTAAACAAAAAGAA 3 32 1 ACAAAATAAA 0.947232 -269 AAGTGTAAAGAAAATTAACTAATAAGGCTGTAGCT 5 39 0 AAATAATAAA 0.971476 -262 TATGTTCTTCAAAACTAACTACAAAGTTTTTGATC 5 138 0 AAATAATAAA 0.971476 -163 AATTTCTAGCAAAGCAAACAAAGAAATTTATCATG 5 191 1 AAAAAAAAAA 0.876715 -110 CTAAAAAACAACAATTAGCTAAGAAAAGTTAT 5 279 1 ACATAGTAAA 0.930363 -22 *** *** ** ** Masking position 7 Map Score: 7.23494 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 78 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 TGCAGTTTTATTATAAAAGAAATAACTAAC 2 27 1 TTATAAAAGA 0.787417 -274 TGCAATCTAGTTATAAAAAACTCACCTAAA 2 123 1 TTATAAAAAA 0.85495 -178 CTAAGAACGCTTCTAAAAAGCTTTTTTGGT 2 167 0 TTCTAAAAAG 0.751744 -134 CTTAAACGTTATCTTCAAGAAAAAGCCTAA 2 244 0 ATCTTCAAGA 0.831823 -57 TTGATAGAAGATATTCAAAACCATGAAGTT 2 278 0 ATATTCAAAA 0.743663 -23 GTTAATGTATTTCTCAAAGAAG 3 289 1 TTCTCAAAGA 0.924089 -12 ATTTGAAATAATATCCAAAAGTGTAAAGAA 5 62 0 ATATCCAAAA 0.777961 -239 TGAACAATACCTCTTAAAAAAGAGGAATAC 5 91 1 CTCTTAAAAA 0.899174 -210 CTCTTTTATGTTCTTCAAAACTAACTACAA 5 149 0 TTCTTCAAAA 0.936928 -152 TTAATTTAGTCTCTCAAAAATTGAGAGCTA 5 239 0 CTCTCAAAAA 0.916637 -62 AAATTAGTTTTTCTAAAAAACAACAATTAG 5 267 1 TTCTAAAAAA 0.941048 -34 ********** Masking position 7 Map Score: 6.38088 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 124 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 CCAACAGATAACCTATAAGGGTCAACTGCT 1 34 0 ACCTATAAGG 0.971462 -68 TAAAAAACTCACCTAAAAGGTAGTTATTAA 2 136 1 ACCTAAAAGG 0.98945 -165 AGTTATTAACACCAAAAAAGCTTTTTAGAA 2 157 1 ACCAAAAAAG 0.867281 -144 AAAACTAGTAAACAAAAAGAAGGGGATTTT 3 46 1 AACAAAAAGA 0.861878 -255 TGTCGAACGGAAATAAAAGACTAGCTACAG 5 17 1 AAATAAAAGA 0.731959 -284 AAGAAAATTAACTAATAAGGCTGTAGCTAG 5 37 0 ACTAATAAGG 0.767997 -264 GTTTTGAAGAACATAAAAGAGAAAACAGGG 5 158 1 ACATAAAAGA 0.909167 -143 AAAAATTGAGAGCTAAAAGGATGTTGTCCA 5 224 0 AGCTAAAAGG 0.955604 -77 ********** Masking position 5 Map Score: 4.38085 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 150 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AAGCAAAAATACCAGCAGTTGACCCTTATAGGTTAT 1 21 1 ACGTTGACCT 0.988709 -81 TTTGGCGCTTACTAGTTCTTGTAACCATTTATTAGT 1 73 1 ACGTTGTACC 0.841771 -29 ATATTCAAAACCATGAAGTTGATACTTAAACGTTAT 2 262 0 CCGTTGAACT 0.918976 -39 AACGCATCCAACACGACTTTGACCCTAACCAGTTTC 3 210 0 ACGTTGACCT 0.98871 -91 CACGCACGCCAAGTGGAATTGTACATTAT 4 34 1 AAGTTGTCAT 0.972066 -19 CCTCTTTTTTAAGAGGTATTGTTCATTTGAAATAAT 5 80 0 AAGTTGTCAT 0.972072 -221 AAACTAACTACAAAGTTTTTGATCATGTGAGCATAC 5 126 0 CAGTTGACAT 0.951714 -175 TTGAGAGCTAAAAGGATGTTGTCCATGATAAATTTC 5 213 0 AAGTTGTCAT 0.972072 -88 ** * **** *** Masking position 9 Map Score: 4.2388 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 35 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 TTGCTCGAATAACACGCATAAAAGTGCTTA 3 74 1 AACACGCATA 0.954969 -227 GCTTAATCTTAGCACGCATAGTACTTTTAA 3 99 1 AGCACGCATA 0.988273 -202 CATCGCTAAAATCACGCGGATTGAGCAAAT 3 138 1 ATCACGCGGA 0.950578 -163 CAGTCTAGTGCGCACGCGTATACACGCACG 4 12 1 CGCACGCGTA 0.992909 -41 CGCGTATACACGCACGCCAAGTGGAATTGT 4 26 1 CGCACGCCAA 0.968015 -27 ********** Masking position 4 Map Score: 2.1906 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 TGGTATTTTTGCTTTGATTGTTAT 1 5 0 GCTTTGATTG 0.960713 -97 CTTTTTAGAAGCGTTCTTAGTTTCAATTAA 2 177 1 GCGTTCTTAG 0.933282 -124 GCATTGATAGAAGATATTCA 2 291 0 GCATTGATAG 0.978552 -10 CGTGTTGGATGCGTTGAAAGTCAGCTGCGT 3 231 1 GCGTTGAAAG 0.974244 -70 TTCTTTGTTTGCTTTGCTAGAAATTCATCC 5 186 0 GCTTTGCTAG 0.97925 -115 ********** Masking position 5 Map Score: 1.16907 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 22 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 GGTTACAAGAACTAGTAAGCGCCAAAATAAA 1 68 0 ACTAGTAGCG 0.98 -34 ATAATAAAACTGCAGTTAGCGGAATGGGAC 2 10 0 TGCAGTTGCG 0.967944 -291 TTCTATACTGAGCAGGAGGCGACTAAAATAG 2 74 1 AGCAGGAGCG 0.977781 -227 AAGATTAAGCACTTTTATGCGTGTTATTCGA 3 78 0 ACTTTTAGCG 0.7351 -223 AACTTTTAAAAGTACTATGCGTGCTAAGATT 3 103 0 AGTACTAGCG 0.953865 -198 TTTGACCCTAACCAGTTTCCGTATGACTGGG 3 198 0 ACCAGTTCCG 0.889115 -103 GTCAAAGTCGTGTTGGATGCGTTGAAAGTCA 3 223 1 TGTTGGAGCG 0.863607 -78 AATGTACAATTCCACTTGGCGTGCGTGTATA 4 30 0 TCCACTTGCG 0.927236 -23 ******* *** Masking position 10 Map Score: 0.860708 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 96 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 ********** No masking Map Score: -3.45081e-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 9 ********** No masking Map Score: -3.45081e-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 10 ********** No masking Map Score: -3.45081e-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