AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_mgen_reg_300.orf -o00380_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 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #2 MG081 55 ribosomal protein L11 (rpl11) #3 MG087 28 ribosomal protein S12 (rpS12) #4 MG090 51 ribosomal protein S6 (rpS6) #5 MG094 49 replicative DNA helicase (dnaB) #6 MG096 182 conserved hypothetical protein #7 MG097 56 uracil DNA glycosylase (ung) #8 MG098 99 Glu-tRNA amidotransferase subunit gatC-related protein #9 MG126 35 tryptophanyl-tRNA synthetase (trpS) #10 MG466 25 ribosomal protein L34 (rpL34) #11 MG468.1 62 ABC transporter, ATP-binding protein #12 MG469 300 chromosomal replication initiator protein (dnaA) Motif number 1 CATTTTTTTATAAAATAATCAAGAACATCAGC 1 31 1 TAAAATATCA 0.971905 -203 TTTAAAATTTTCCAAAAATGTGGG 2 3 1 TAAAATTTCA 0.99291 -53 AAATTAATGGTAAAATTATTCATTAAACTTTC 6 46 1 TAAAATTTTA 0.971861 -137 GACAATTAAATAACATATTTTAAAGATCTAGA 6 140 0 TAACATATTA 0.652038 -43 AAATAAACTTTAAATTTATCTAGGTAAAAGTA 7 35 0 TAAATTTTCA 0.947288 -22 AACAACCTTGTAAAATTATTTAACTAAGTGAT 8 57 1 TAAAATTTTA 0.944513 -43 CAAAATTAAAATTTTCTAATAGTGTTCT 11 7 1 TAAAATTTCA 0.986586 -56 TCAAGAGGAACAAAATTTTCAATATCATAATA 12 32 1 CAAAATTTCA 0.98219 -269 GCAAAAAAATCAAAATTTTCAACAACAATTCA 12 77 1 CAAAATTTCA 0.98219 -224 GAATGATAGTTAAAATTCTCGAAATTGGGATA 12 257 0 TAAAATTTCA 0.993085 -44 TATTCTTCTATAACATTGTCAAGAATGATAGT 12 279 0 TAACATTTCA 0.982195 -22 ******* ** * Masking position 3 Map Score: 22.8524 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 19 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 ACCAGTACCATTTCCAAAAAACTGAGAACCTGAAA 1 176 1 TTTCCAAATA 0.954862 -58 TTTAAAATTTTCCAAAAATGTGGGAGCTAATTA 2 9 1 TTTCCAAATG 0.86683 -47 TCAATGAGTTTTTCCAAAAAGTTTTT 4 36 1 TTTCCAAATT 0.946814 -16 TTTTAAATATGCAAATGATAGCAAC 5 1 1 TTTTAAAAAA 0.888225 -49 TAAACTTTTCTTTTCAAAACTGAATGGCTAAAATT 6 12 0 TTTTCAAAAT 0.977695 -171 TTAGTTGTAGTTTTCAATACTGTTTGTATTTCGAA 6 82 1 TTTTCAAATT 0.969552 -101 AACTACGAATTTTTTAAAATGAACTTCGAAATACA 6 106 0 TTTTTAAAAT 0.79294 -77 AAATAACATATTTTAAAGATCTAGAACTACGAATT 6 130 0 TTTTAAAAAA 0.889201 -53 AAGAGAGATATTTTCAAGAGGAACAAAATTTTCAA 12 19 1 TTTTCAAAAA 0.981144 -282 AGGAACAAAATTTTCAATATCATAATAATGGTTTC 12 37 1 TTTTCAAATA 0.974235 -264 AAAATCAAAATTTTCAACAACAATTCACACAACCA 12 82 1 TTTTCAAAAT 0.977697 -219 TTCTATAACATTGTCAAGAATGATAGTTAAAATTC 12 271 0 TTGTCAAAAA 0.899424 -30 ******* * * * Masking position 7 Map Score: 13.8588 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 234 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 TATCACTAAATTTATGTTTGGTTTCAAATGAA 1 73 1 TTTTTTTGGT 0.98863 -161 GCTGGTTACTTTTGTTTCAGGTAACCAGTACC 1 153 1 TTTTTCAGGT 0.987044 -81 AAAGAACCTGTTTTTTTCAGGTTCTCAGTTTT 1 193 0 TTTTTCAGGT 0.987044 -41 TCTTTTTTTATTTCTATTTAGTAA 1 220 1 TTTTTTTAGT 0.959546 -14 TAAAGTTATATTTTTATTAAGTAT 4 3 0 TTTTTTAAGT 0.968637 -49 AAAATATCTCTCTTTTTTTGGT 12 1 0 TCTTTTTGGT 0.963969 -300 TCCTGGTATTTTTGTTTTAGGTTGGGGAGGAA 12 124 0 TTTTTTAGGT 0.991245 -177 *** * ****** Masking position 7 Map Score: 8.38872 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 33 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 GTTACCTGAAACAAAAGTAACCAGCTTCTAAA 1 146 0 ACAAAGAACC 0.835021 -88 AAATAGAAATAAAAAAAGAACCTGTTTTTTTC 1 207 0 AAAAAAAACC 0.977227 -27 ATACTTAATAAAAATATAACTTTACTCAATG 4 10 1 AAAAAAAACT 0.964169 -42 AACAGTATTGAAAACTACAACTAACAAGGAAA 6 74 0 AAAACAAACT 0.943989 -109 TATGAAATTAAAAAAGACAATTAAATAACATA 6 155 0 AAAAAAAATT 0.701576 -28 TTAAAAACAAAGCTGTAGTTGACA 8 3 1 AAAAAAAGCT 0.956888 -97 ATTGATTAGAAAAACAACAACCTTGTAAAATT 8 42 1 AAAACAAACC 0.964127 -58 TAAGTCATCTAAAAAAATACCCTGAGAACACT 11 31 0 AAAAAAACCC 0.960474 -32 ACCAAAAAAAGAGAGATATTTTCAAGA 12 6 1 AAAAAAAGAT 0.659765 -295 AACAATTCACACAACCACAGCCTATTCCTCCC 12 100 1 ACAACAAGCC 0.932817 -201 CCAACCTAAAACAAAAATACCAGGAATAGTTC 12 131 1 ACAAAAACCA 0.701889 -170 ***** * **** Masking position 4 Map Score: 7.67254 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 219 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AAAATGATACTAATAACGATTACTAG 1 5 0 TAAAAGATTA 0.828541 -229 TGATTACAATAAAGCAGGATTTATAATCCAAC 1 105 0 AAACAGATTT 0.702866 -129 TTCTAAATCTAAAGCATGATTACAATAAAGCA 1 121 0 AAACAGATTA 0.918587 -113 CAGTTTTGAAAAGAAAAGTTTAAATTAATGGT 6 25 1 AAGAAGTTTA 0.954278 -158 TACAACTAACAAGGAAAGTTTAATGAATAATT 6 59 0 AAGAAGTTTA 0.954289 -124 AAATAAACTTTAAATTTATCTA 7 45 0 AAAAACTTTA 0.953306 -12 TAAAATAACCTTTAATTACCCTAT 9 3 1 AAAAACTTTA 0.953306 -33 AAACAATCATTAAGTCATCTAA 11 51 0 AAAAACATTA 0.961728 -12 TTTTTGCTGTAAGAAACCATTATTATGATATT 12 52 0 AAGAACATTA 0.954054 -249 *** ** ***** Masking position 6 Map Score: 6.47251 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 164 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GCACATGATCTTTATCACTAAATTTATGTTTGGT 1 61 1 TTTTCATATT 0.931244 -173 AAATATAACTTTACTCAATGAGTTTTTCCAAAAA 4 22 1 TTATCATATT 0.977201 -30 CAATTTTAGCCATTCAGTTTTGAAAAGAA 6 6 1 TTACCATATT 0.972492 -177 AATGAATAATTTTACCATTAATTTAAACTTTTCT 6 36 0 TTTCCATATT 0.917843 -147 AATGGTAAAATTATTCATTAAACTTTCCTTGTTA 6 51 1 TTATCATACT 0.899381 -132 TAAGAAATTTTTGATCAGTTACTTTTACCTAGAT 7 16 1 TTGTCATATT 0.919251 -41 AAATAAACTTTAAATTTATCTAGGTA 7 41 0 ATAACTTATT 0.645944 -16 CAATTAAGTAATAATCACTTAGTTAAATAATTTT 8 68 0 ATATCATATT 0.950998 -32 TAACCTTTAATTACCCTATCAATTCTAATA 9 16 1 TTACCTTATT 0.941204 -20 ACTTTTTGTCATACTCTTTGACTTGTATAGAAGT 12 199 0 ATATCTTATT 0.897832 -102 *** *** * * ** Masking position 9 Map Score: 7.8722 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 110 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 CCTGAAACAAAAGTAACCAGCTTCTAAATC 1 144 0 AAGTAACCAG 0.946175 -90 CTTTTGTTTCAGGTAACCAGTACCATTTCC 1 161 1 AGGTAACCAG 0.922053 -73 TCCAAAAAACTGAGAACCTGAAAAAAACAG 1 188 1 TGAGAACCTG 0.922053 -46 AGAAATAAAAAAAGAACCTGTTTTTTTCAG 1 205 0 AAAGAACCTG 0.975838 -29 TAAAATAACCTTTAATTACCCT 9 3 1 AAATAACCTT 0.886219 -33 TTATAATCACCTGATTAATTGTT 10 4 1 TAATCACCTG 0.88936 -22 TCATCTAAAAAAATACCCTGAGAACACTAT 11 29 0 AAATACCCTG 0.948659 -34 ********** Masking position 7 Map Score: 1.74037 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 69 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 ********** No masking Map Score: -2.07235e-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: -2.07235e-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: -2.07235e-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