AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_mgen_reg_100.orf -o00790_mgen_100.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MG070 110 ribosomal protein S2 (rpS2) #2 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #3 MG081 55 ribosomal protein L11 (rpl11) #4 MG087 28 ribosomal protein S12 (rpS12) #5 MG090 51 ribosomal protein S6 (rpS6) #6 MG094 49 replicative DNA helicase (dnaB) #7 MG227 300 thymidylate synthase (thyA) #8 MG244 300 DNA helicase II, putative #9 MG272 249 dihydrolipoamide acetyltransferase (pdhC) Motif number 1 TTTATGGCTTTTAGTTATTATCGAGTTTTA 1 15 0 TTAGTTATTA 0.650165 -96 CCATAAAACCTTGGTTTTGTGGTTTTTAGC 1 38 1 TTGGTTTTGT 0.926298 -73 GTTATTAGTATCATTTTTTTATAAAATAAT 2 20 1 TCATTTTTTT 0.66032 -214 GCTGATGTTCTTGATTATTTTATAAAAAAA 2 33 0 TTGATTATTT 0.731738 -201 TTTCAGGTTCTCAGTTTTTTGGAAATGGTA 2 181 0 TCAGTTTTTT 0.799495 -53 AAAAAAGAACCTGTTTTTTTCAGGTTCTCA 2 198 0 CTGTTTTTTT 0.929846 -36 AAAAAACAGGTTCTTTTTTTATTTCTATTT 2 209 1 TTCTTTTTTT 0.743439 -25 GGATAGGTGGTTGTTTTTTTGGCTGGGGAG 7 172 0 TTGTTTTTTT 0.967409 -129 GCTTTTTATTTTGTTTTTTTAATAAACATT 7 242 0 TTGTTTTTTT 0.967409 -59 GAAATTGTCTTTTAGACAGGTTAT 7 287 0 TTGTCTTTTA 0.817871 -14 AGCGAAGCGCTTAATTTTTTCACTAATTTA 8 18 1 TTAATTTTTT 0.810038 -283 ACAATTTTGATTAGTTTTTTACAACTGATT 8 87 1 TTAGTTTTTT 0.95078 -214 TTTTTTACAACTGATTTTTATTGGTTATTT 8 101 1 CTGATTTTTA 0.739939 -200 CTGATTTTTATTGGTTATTTTTGTTTTAGT 8 111 1 TTGGTTATTT 0.925129 -190 TTTAAGCTAGTTGGTTTTGATTTTAAAGTG 8 200 0 TTGGTTTTGA 0.856287 -101 AGGTTGATTGTTGGTTTTTAAGCTAGTTGG 8 216 0 TTGGTTTTTA 0.966516 -85 TTACCTAGCTTTATTTTTTAGAGCTAGGTA 9 29 1 TTATTTTTTA 0.817003 -221 AGTTTAGTTACTGGCTTTTTAGTTGTTAGA 9 166 0 CTGGCTTTTT 0.896649 -84 AGTAACTAAACTGGCTTTTTTTATTTGTTA 9 184 1 CTGGCTTTTT 0.896649 -66 ********** Masking position 6 Map Score: 21.4827 Number of sites scoring better than the average of aligned sites = 900 Number in coding regions = 813 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 TCAATAAAACTCGATAATAACTAAAA 1 5 1 TAAAACTGTA 0.67793 -106 TAAAAGCCATAAAACCTTGGTTTTGTGGTTTT 1 32 1 AAAACCTGTT 0.661025 -79 TGGTTTCAAATGAAGTTGGATTATAAATCCTG 2 91 1 TGAAGTTGTT 0.859515 -143 ATGATTACAATAAAGCAGGATTTATAATCCAA 2 106 0 TAAAGCAGTT 0.96218 -128 CTTCTAAATCTAAAGCATGATTACAATAAAGC 2 122 0 TAAAGCAGTT 0.962183 -112 CTTTAGATTTAGAAGCTGGTTACTTTTGTTTC 2 139 1 AGAAGCTGTA 0.919431 -95 ATAGACAACTGAAGTATTCTAACAAAAT 4 8 0 TGAAGTATTA 0.308045 -21 ACTCATTGAGTAAAGTTATATTTTTATTAAGT 5 13 0 TAAAGTTTTT 0.630037 -39 ATGTCAGGTGAAAAGTTAGGTATAAACACCCA 7 12 0 AAAAGTTGTA 0.85574 -289 ACATCTGAACAGGAGCAGGGTATCGCAAACAA 7 40 1 AGGAGCAGTA 0.603029 -261 TGGAGTTTGGTAAAGCAGGATAGGTGGTTGTT 7 187 0 TAAAGCAGTA 0.957815 -114 AAACAAAATAAAAAGCGGTTTTATACAATGTA 7 256 1 AAAAGCGTTT 0.529518 -45 GTATCTCTTGTAAAGCTTGTTTTTCAGAACTA 8 137 0 TAAAGCTGTT 0.978061 -164 GTTTTGATTTTAAAGTGTGTTTTTCTTGAACC 8 185 0 TAAAGTGGTT 0.819121 -116 CTCTAAAAAATAAAGCTAGGTAACTATATTTT 9 20 0 TAAAGCTGTA 0.975505 -230 CTTTATTTTTTAGAGCTAGGTACCTCATTTCA 9 37 1 TAGAGCTGTA 0.90286 -213 AACAAATAAAAAAAGCCAGTTTAGTTACTGGC 9 181 0 AAAAGCCGTT 0.838476 -69 ******* * ** Masking position 4 Map Score: 15.4235 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 247 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 ATATAACTTTACTCAATGAGTTTTTCCAAAAAG 5 24 1 ACTAAGAGTT 0.961422 -28 TGATAGCAACATTGAACGTGCTGAAAGACGTTT 6 26 1 ATTAAGTGTG 0.965689 -24 AAGAATTGGGATTAAACGTGTTGCTACTACTAC 7 111 0 ATTAAGTGTG 0.965689 -190 TAATAAAGTCACTCAAGGTGGTGGCTCCCCAGC 7 148 1 ACTAAGTGTG 0.984467 -153 CACTGGTGGGACTGATGGAGTTTGGTAAAGCAG 7 201 0 ACTATGAGTT 0.817058 -100 TTTCTTGAACCATAAAGGTGTTTGACAGTATCT 8 163 0 CATAAGTGTT 0.870994 -138 TGTTATTAATTAATGAGTTTTTCCACTTCA 8 281 0 AATAAGAGTT 0.94065 -20 TCATTTCATAAATTAAAGTGATGGAAGACAACA 9 61 1 AATAAGTGTG 0.975654 -189 *** ** *** ** Masking position 5 Map Score: 5.26948 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 34 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 CTGGTTACTTTTGTTTCAGGTAACCAGTACCA 2 154 1 TTGTTTCGTA 0.930761 -80 TATTGTTACCTTGTTTGCGATACCCTGCTCCT 7 50 0 TTGTTTGGTA 0.961149 -251 ATGGTTCTAATTGTTATCGCTATTGCATTAGG 8 54 0 TTGTTATGTA 0.974906 -247 CTAATCAAAATTGTTATGGTTCTAATTGTTAT 8 69 0 TTGTTATGTC 0.979133 -232 TTGGTTATTTTTGTTTTAGTTCTGAAAAACAA 8 121 1 TTGTTTTGTC 0.972999 -180 CTAGCTTTATTTTTTAGAGCTAGGTACCTCAT 9 33 1 TTTTTAGGTA 0.806884 -217 CTTTTTTTATTTGTTATAGATCACTACTATTA 9 198 1 TTGTTATGTC 0.979133 -52 ******* * ** Masking position 5 Map Score: 5.00701 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 60 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 ATTATTGCAGTTTTACTGCATAATGTAAAA 1 82 1 TTTTACTGCA 0.61961 -29 AGTATCATTTTTTTATAAAATAATCAAGAA 2 26 1 TTTTATAAAA 0.489476 -208 AACCAGTACCATTTCCAAAAAACTGAGAAC 2 175 1 ATTTCCAAAA 0.736204 -59 TTTAAAATTTTCCAAAAATGTGGGAGC 3 8 1 TTTTCCAAAA 0.934032 -48 CTCAATGAGTTTTTCCAAAAAGTTTTT 5 35 1 TTTTCCAAAA 0.934032 -17 AGGTTATACATTGTATAAAACCGCTTTTTA 7 264 0 TTGTATAAAA 0.5858 -37 GTAAAGCTTGTTTTTCAGAACTAAAACAAA 8 130 0 TTTTTCAGAA 0.848197 -171 TAAAGTGTGTTTTTCTTGAACCATAAAGGT 8 177 0 TTTTCTTGAA 0.728516 -124 CACTTTTTTAAAATATAGTTACC 9 4 1 TTTTTTAAAA 0.614113 -246 TTGTCTTACTTTTTACAGCAGCTGTTGCAC 9 128 0 TTTTACAGCA 0.867478 -122 GACAAAATTTTTGTCTAACAACTAAAAAGC 9 153 1 TTGTCTAACA 0.735373 -97 ********** Masking position 10 Map Score: 4.8445 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 261 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 CCTGAAACAAAAGTAACCAGCTTCTAAATC 2 144 0 AAGTAACCAG 0.957628 -90 CTTTTGTTTCAGGTAACCAGTACCATTTCC 2 161 1 AGGTAACCAG 0.991592 -73 ATCGCAAACAAGGTAACAATAATGGCATCT 7 61 1 AGGTAACAAT 0.950473 -240 AAATAAAGCTAGGTAACTATATTTTAAAAA 9 15 0 AGGTAACTAT 0.971298 -235 TTATGAAATGAGGTACCTAGCTCTAAAAAA 9 42 0 AGGTACCTAG 0.97171 -208 ********** Masking position 5 Map Score: 3.07011 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 7 TAAACAAGCTAAAAACCACAAAACCAAGGT 1 45 0 AAAAACCACA 0.810517 -66 TACCATTTCCAAAAAACTGAGAACCTGAAA 2 181 1 AAAAAACTGA 0.786081 -53 CTGAGAACCTGAAAAAAACAGGTTCTTTTT 2 197 1 GAAAAAAACA 0.929499 -37 AAACTTTTTGGAAAAACTCATTGAGTAAAG 5 30 0 GAAAAACTCA 0.978161 -22 GCTCCCCAGCCAAAAAAACAACCACCTATC 7 171 1 CAAAAAAACA 0.717083 -130 ATGTTTATTAAAAAAACAAAATAAAAAGCG 7 243 1 AAAAAACAAA 0.881577 -58 CTAAATTAGTGAAAAAATTAAGCGCTTCGC 8 19 0 GAAAAAATTA 0.590013 -282 AATCAGTTGTAAAAAACTAATCAAAATTGT 8 87 0 AAAAAACTAA 0.862345 -214 TTTTAGTTCTGAAAAACAAGCTTTACAAGA 8 134 1 GAAAAACAAG 0.766631 -167 TATGGTTCAAGAAAAACACACTTTAAAATC 8 182 1 GAAAAACACA 0.981558 -119 TGATGAAGTGGAAAAACTCATTAATTAATA 8 278 1 GAAAAACTCA 0.978161 -23 ********** Masking position 5 Map Score: 9.40392 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 197 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TAATCCAACTTCATTTGAAACCAAACATAA 2 84 0 TCATTTGAAA 0.866981 -150 TGTTCAGATGTCAGGTGAAAAGTTAGGTAT 7 21 0 TCAGGTGAAA 0.987119 -280 ATCTCCTTGACCAGGTGAAACCTAGTAGTA 7 87 1 CCAGGTGAAA 0.988057 -214 CCAATAAAAATCAGTTGTAAAAAACTAATC 8 95 0 TCAGTTGTAA 0.959574 -206 AGCTAATTTACCAGGCGTAATAGCTCTTGA 8 251 1 CCAGGCGTAA 0.96297 -50 ********** Masking position 3 Map Score: 1.5195 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 38 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 ********** No masking Map Score: 1.68642e-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: 1.68642e-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 11 ********** No masking Map Score: 1.68642e-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