AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_mgen_reg_300.orf -o00790_mgen_300.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 MG069 300 PTS system, glucose-specific IIABC component (ptsG) #2 MG070 110 ribosomal protein S2 (rpS2) #3 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #4 MG081 55 ribosomal protein L11 (rpl11) #5 MG087 28 ribosomal protein S12 (rpS12) #6 MG090 51 ribosomal protein S6 (rpS6) #7 MG094 49 replicative DNA helicase (dnaB) #8 MG227 300 thymidylate synthase (thyA) #9 MG244 300 DNA helicase II, putative #10 MG272 249 dihydrolipoamide acetyltransferase (pdhC) #11 MG274 27 pyruvate dehydrogenase component E1, subunit alpha (pdhA) #12 MG275 82 NADH oxidase (nox) #13 MG277 42 conserved hypothetical protein Motif number 1 AACATATGCTCTTTTAGTTGTTTTTGGAATTTTATTAG 1 26 1 CTTTTTTTGA 0.703028 -275 ACTAGGATTTTTATTTTGAGCTTTAAAAATTTCACTTA 1 74 1 TTTTATTTAA 0.884479 -227 AATTTGACCTTTCTTTTGTTCTTTAAGTGAAATTTTTA 1 97 0 TTTTTTTTGT 0.942539 -204 TAAAACTAATTTGTTGTTTCTTTTTCATCAACTCCCTC 1 181 0 TTTTTTTTAT 0.965181 -120 GGTTTTGTGGTTTTTAGCTTGTTTATAACAATATTATT 2 50 1 TTTTTTTTAA 0.974041 -61 TGTGCTGATGTTCTTGATTATTTTATAAAAAAATGATA 3 28 0 TTTTTTTTAA 0.973465 -206 TATCACTAAATTTATGTTTGGTTTCAAATGAAGTTGGA 3 73 1 TTATTTTTAA 0.933331 -161 AAAAAACAGGTTCTTTTTTTATTTCTATTTAGTAA 3 209 1 TTTTTTTTAT 0.965181 -25 AGCTCCCACATTTTTGGAAAATTTTAAA 4 1 0 TTTTATTTAA 0.884476 -55 GATGCCATTATTGTTACCTTGTTTGCGATACCCTGCTC 8 52 0 TTTTTTTTGA 0.957127 -249 AAACCGCTTTTTATTTTGTTTTTTTAATAAACATTTTA 8 239 0 TTTTTTTTAT 0.965181 -62 AGCGCTTAATTTTTTCACTAATTTAGATAAGCCTAATG 9 23 1 TTTTTTTTAT 0.965169 -278 CATAACAATTTTGATTAGTTTTTTACAACTGATTTTTA 9 83 1 TTATTTTTAA 0.932744 -218 ACAACTGATTTTTATTGGTTATTTTTGTTTTAGTTCTG 9 107 1 TTATTTTTGT 0.858891 -194 CTGGATCAGGTTGATTGTTGGTTTTTAAGCTAGTTGGT 9 215 0 TTATTTTTAA 0.93333 -86 AAACTGGCTTTTTTTATTTGTTATAGATCACTACTATT 10 191 1 TTTTTTATAT 0.664794 -59 ATATTTCTATGCTAATTTAAAACTAAG 11 6 0 TTTATTTTAA 0.727427 -22 TGTGCAGTAGTGATTCGATCTTTTAAAATTAAGCTTTT 12 12 0 TGTTTTTTAA 0.800023 -71 TACTTAATATTTATATAAAATTTAAGTTATTAAAAAT 13 10 1 TTATATTTGT 0.552624 -33 ** ** * *** ** Masking position 12 Map Score: 25.9556 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 248 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 TAGTAATTTGACCTTTCTTTTGTTCTTTAAGTG 1 106 0 ACCTTTTTTT 0.937978 -195 TCCCTCTAGGAACTTCATTTTTAAGTGAGTTAT 1 154 0 AACTTTTTTA 0.967401 -147 AAGAAACAACAAATTAGTTTTATTTTTGCTTGC 1 197 1 AAATTTTTTT 0.591934 -104 TTTAAAACTACTAAATTTTATTAACCAAACA 1 280 0 TACTATTTTT 0.555857 -21 AAGCCATAAAACCTTGGTTTTGTGGTTTTTAGC 2 35 1 ACCTTTTTTT 0.937978 -76 TGTGGTTTTTAGCTTGTTTATAACAATATTATT 2 55 1 AGCTTTTATA 0.613846 -56 TTTATAATCCAACTTCATTTGAAACCAAACATA 3 85 0 AACTTTTTGA 0.758851 -149 ATAAAAAAAGAACCTGTTTTTTTCAGGTTCTCA 3 198 0 AACCTTTTTT 0.871527 -36 GGGTGTTTATACCTAACTTTTCACCTGACATCT 8 13 1 ACCTATTTTA 0.785957 -288 CATTGTATAAAACCGCTTTTTATTTTGTTTTTT 8 253 0 AACCGTTTTT 0.790238 -48 AGCAGCGAAGCGCTTAATTTTTTCACTAATTTA 9 15 1 CGCTTTTTTT 0.745486 -286 AGTTTTTTACAACTGATTTTTATTGGTTATTTT 9 99 1 AACTGTTTTT 0.948054 -202 TCTCTTGTAAAGCTTGTTTTTCAGAACTAAAAC 9 133 0 AGCTTTTTTA 0.956931 -168 AAAGCTAGGTAACTATATTTTAAAAAAGTG 10 8 0 AACTATTTTA 0.888635 -242 ATAGTTACCTAGCTTTATTTTTTAGAGCTAGGT 10 25 1 AGCTTTTTTT 0.960945 -225 CCAGTTTAGTTACTGGCTTTTTAGTTGTTAGAC 10 165 0 TACTGTTTTA 0.700072 -85 CCAGTAACTAAACTGGCTTTTTTTATTTGTTAT 10 182 1 AACTGTTTTT 0.948054 -68 CAAAAGCTTAATTTTAAAAGATCGAAT 12 5 1 AGCTTTTTTA 0.956931 -78 TATTTTTAATAACTTAAATTTTATATAAATATT 13 16 0 AACTTATTTA 0.679813 -27 ***** **** * Masking position 9 Map Score: 16.9123 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 421 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 TCAATAAAACTCGATAATAACTAAA 2 5 1 TAAAACTGAT 0.770473 -106 TTTTGTGGTTTTTAGCTTGTTTATAACAATA 2 52 1 TTTAGCTGTT 0.829887 -59 ATGATTACAATAAAGCAGGATTTATAATCCA 3 107 0 TAAAGCAGAT 0.961713 -127 CTTCTAAATCTAAAGCATGATTACAATAAAG 3 123 0 TAAAGCAGAT 0.961713 -111 CAAACGTCTTTCAGCACGTTCAATGTTGCT 7 30 0 TTCAGCAGTT 0.809998 -20 TGGAGTTTGGTAAAGCAGGATAGGTGGTTGT 8 188 0 TAAAGCAGAT 0.961713 -113 GTATCTCTTGTAAAGCTTGTTTTTCAGAACT 9 138 0 TAAAGCTGTT 0.981304 -163 TTGTTGGTTTTTAAGCTAGTTGGTTTTGATT 9 208 0 TTAAGCTGTT 0.968698 -93 CTCTAAAAAATAAAGCTAGGTAACTATATTT 10 21 0 TAAAGCTGGT 0.972466 -229 CTTTATTTTTTAGAGCTAGGTACCTCATTTC 10 37 1 TAGAGCTGGT 0.891916 -213 CAGTAATTTTTTAAGCTATTTAAGGATAATT 12 50 0 TTAAGCTTTT 0.709165 -33 ******* *** Masking position 4 Map Score: 10.7383 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 83 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 ATTGGACTAGGATTTTTATTTTGAGCTTTAAA 1 69 1 GATTTATTTT 0.774486 -232 ACAACAAATTAGTTTTATTTTTGCTTGCAATA 1 202 1 AGTTTTTTTT 0.892898 -99 ATAAAACCTTGGTTTTGTGGTTTTTAGCTTGT 2 40 1 GGTTTTGGTT 0.781178 -71 TTTAGAAGCTGGTTACTTTTGTTTCAGGTAAC 3 146 1 GGTTCTTTGT 0.85204 -88 GTTTTTTTCAGGTTCTCAGTTTTTTGGAAATG 3 184 0 GGTTTAGTTT 0.937911 -50 GAAAAAAACAGGTTCTTTTTTTATTTCTATTT 3 207 1 GGTTTTTTTT 0.983607 -27 CATTGAGTAAAGTTATATTTTTATTAAGTAT 6 10 0 AGTTTTTTTT 0.892898 -42 CAGGATAGGTGGTTGTTTTTTTGGCTGGGGAG 8 172 0 GGTTTTTTTT 0.983607 -129 GTATAAAACCGCTTTTTATTTTGTTTTTTTAA 8 250 0 GCTTTATTTT 0.835798 -51 AAATTGTTATGGTTCTAATTGTTATCGCTATT 9 62 0 GGTTTATTGT 0.960578 -239 GATTTTTATTGGTTATTTTTGTTTTAGTTCTG 9 113 1 GGTTTTTTGT 0.971052 -188 TAAGCTAGTTGGTTTTGATTTTAAAGTGTGTT 9 196 0 GGTTTATTTT 0.977572 -105 **** * ***** Masking position 4 Map Score: 14.5396 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 118 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 CAAAAGAAAGGTCAAATTACTAATGATTTGACT 1 117 1 GTAATACTAA 0.917544 -184 ATGATTTGACTTCCAATAACTCACTTAAAAATG 1 139 1 TTAAAACTCA 0.965496 -162 ATTCCTAGCATTAAAAAAACTATTGCAAGCAAA 1 221 0 TTAAAACTAT 0.783536 -80 TTTAAAACTACTAAATTTTATTAA 1 287 0 TTAATACTAA 0.915723 -14 ACTGCATAATGTAAAATTACACAGC 2 96 1 GTAATACACA 0.651532 -15 AAAAACTTTTTGGAAAAACTCATTGAGTAAAG 6 30 0 TTAAAACTCA 0.965495 -22 AAAATGTTTATTAAAAAAACAAAATAAAAAGCG 8 240 1 TTAAAACAAA 0.874161 -61 ATCTAAATTAGTGAAAAAATTAAGCGCTTCGCT 9 18 0 GTAAAATTAA 0.695395 -283 AAAAATCAGTTGTAAAAAACTAATCAAAATTGT 9 87 0 TGAAAACTAA 0.842886 -214 TAAAGCTTGTTTTTCAGAACTAAAACAAAAATA 9 126 0 TTCAAACTAA 0.842887 -175 TCTTGATGAAGTGGAAAAACTCATTAATTAATA 9 275 1 GTAAAACTCA 0.966118 -26 CAAAATTTTTGTCTAACAACTAAAAAGCCAGTA 10 155 1 GTAAAACTAA 0.971958 -95 TAACTATTTTTAATAACTTAAATTTTATAT 13 23 0 TTAAAACTTA 0.842818 -20 ** ** ****** Masking position 6 Map Score: 10.677 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 139 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 6 TGAAAAAGAAACAACAAATTAGTTTTATTT 1 192 1 ACAACAAATT 0.758405 -109 TAGCTTGTTTATAACAATATTATTGCAGTT 2 64 1 ATAACAATAT 0.921023 -47 TGATTATTTTATAAAAAAATGATACTAATA 3 22 0 ATAAAAAAAT 0.77094 -212 TTGAAACCAAACATAAATTTAGTGATAAAG 3 70 0 ACATAAATTT 0.51181 -164 CGTTTGTACCACAGCAAAAT 4 46 1 ACAGCAAAAT 0.754717 -10 ATACTTAATAAAAATATAACTTTACTC 6 8 1 ATAAAAATAT 0.879052 -44 TATGCAAATGATAGCAACATTGAACGTGCT 7 18 1 ATAGCAACAT 0.576316 -32 GTTTATTAAAAAAACAAAATAAAAAGCGGT 8 245 1 AAAACAAAAT 0.459885 -56 TGCAATAGCGATAACAATTAGAACCATAAC 9 59 1 ATAACAATTA 0.555302 -242 AATTAGAACCATAACAATTTTGATTAGTTT 9 74 1 ATAACAATTT 0.869352 -227 CAGAACTAAAACAAAAATAACCAATAAAAA 9 115 0 ACAAAAATAA 0.581623 -186 TAGTTGTTAGACAAAAATTTTGTCTTACTT 10 147 0 ACAAAAATTT 0.808626 -103 TTAAATTAGCATAGAAATAT 11 18 1 ATAGAAATAT 0.802514 -10 CTTAAATTTTATATAAATATTAAGTA 13 7 0 ATATAAATAT 0.64229 -36 ********** Masking position 6 Map Score: 3.80452 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 254 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 CTTTTAGTTATTATCGAGTTTTATTGA 2 7 0 TTATGAGTTT 0.677473 -104 ATAACTTTACTCAATGAGTTTTTCCAAAAAG 6 26 1 TCAAGAGTTT 0.936029 -26 TTTCACCTGGTCAAGGAGATGCCATTATTGT 8 76 0 TCAAGAGATG 0.833597 -225 GAATTGGGATTAAACGTGTTGCTACTACTAC 8 111 0 TAAAGTGTTG 0.91151 -190 ATAAAGTCACTCAAGGTGGTGGCTCCCCAGC 8 150 1 TCAAGTGGTG 0.860421 -151 CCAGTGACTGTTAAAATGTTTATTAAAAAAA 8 228 1 TTAAATGTTT 0.65629 -73 TCTTGAACCATAAAGGTGTTTGACAGTATCT 9 163 0 TAAAGTGTTT 0.904831 -138 GGTTTTGATTTTAAAGTGTGTTTTTCTTGAA 9 187 0 TTAAGTGTGT 0.820075 -114 TGTTATTAATTAATGAGTTTTTCCACTTCA 9 281 0 TTAAGAGTTT 0.937218 -20 ATTTCATAAATTAAAGTGATGGAAGACAACA 10 63 1 TTAAGTGATG 0.882109 -187 **** ****** Masking position 3 Map Score: 2.16558 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 152 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 GCATTAAAAAAACTATTGCAAGCAAAAATA 1 217 0 AACTATTGCA 0.954278 -84 TTTATAACAATATTATTGCAGTTTTACTGC 2 71 1 TATTATTGCA 0.875859 -40 ATTATTGCAGTTTTACTGCATAATGTAAAA 2 82 1 TTTTACTGCA 0.72144 -29 TAATTGTTATCGCTATTGCATTAGGCTTAT 9 49 0 CGCTATTGCA 0.948337 -252 TTTTTACAGCAGCTGTTGCACTTAGCGCAT 10 119 0 AGCTGTTGCA 0.841013 -131 AAGATCGAATCACTACTGCACAAATTATCC 12 28 1 CACTACTGCA 0.96456 -55 TAGCTTAAAAAATTACTGCAGCTAAGATAT 12 63 1 AATTACTGCA 0.924299 -20 ********** Masking position 10 Map Score: 0.930309 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 39 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 ********** No masking Map Score: 1.37378e-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: 1.37378e-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 CAACTAAAAGAGCATATGTTGTTTGCATGCA 1 15 0 AGCATTGTTG 0.97619 -286 GGTGTTTGACAGTATCTCTTGTAAAGCTTGT 9 149 0 AGTATTCTTG 0.963644 -152 TACCAGGCGTAATAGCTCTTGATGAAGTGGA 9 259 1 AATAGTCTTG 0.845747 -42 TTGCATTGGCAGCATTTCTTGTTGTCTTCCA 10 82 0 AGCATTCTTG 0.983531 -168 TACTTTTTACAGCAGCTGTTGCACTTAGCGC 10 121 0 AGCAGTGTTG 0.977905 -129 ***** ***** Masking position 7 Map Score: 0.073347 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 13 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 ********** No masking Map Score: 1.37378e-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 13 ********** No masking Map Score: 1.37378e-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 14 ********** No masking Map Score: 1.37378e-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