AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_mgen_reg_300.orf -o00330_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 MG014 239 ABC transporter, ATP-binding protein #2 MG015 46 ABC transporter, ATP-binding protein #3 MG017 65 ATP-dependent RNA helicase, putative #4 MG018 188 ATP-dependent RNA helicase, putative #5 MG019 41 heat shock protein (dnaJ) #6 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #7 MG081 55 ribosomal protein L11 (rpl11) #8 MG087 28 ribosomal protein S12 (rpS12) #9 MG090 51 ribosomal protein S6 (rpS6) #10 MG094 49 replicative DNA helicase (dnaB) #11 MG096 182 conserved hypothetical protein #12 MG097 56 uracil DNA glycosylase (ung) #13 MG098 99 Glu-tRNA amidotransferase subunit gatC-related protein #14 MG283 300 prolyl-tRNA synthetase (proS) #15 MG378 28 arginyl-tRNA synthetase (argS) Motif number 1 GTTATAATAATTAGTTAAATACCCTTAGGATTATGCTTGG 1 145 0 TTGTAATTAA 0.873607 -95 GGTATTTTGGTTAAATTAAAATTGTTATAATAATTAGTTA 1 168 0 TTAAAATTAA 0.932488 -72 TTTAAAATCTTTCAAGAACTTGGTTTTACA 2 1 0 TTAAATTTTA 0.769899 -46 TTTAATAGTGTTGAAAGACAAACATTATTAATTTTTGATC 3 16 1 TTAAAATTAA 0.937186 -50 CGGTTGAAGTTTGATGTATTAGTTTTTTGAG 4 2 0 TTATAATTTA 0.970878 -187 CGTTTACTTTTTTATGAACAAGCACTACAAAGGTTTTATG 4 40 1 TTATAACTAA 0.695166 -149 CTACAAAGGTTTTATGAAGAATTATTTCAAATAGATTATT 4 64 1 TTATAATTTA 0.965819 -125 TTTCAAATAGATTATTTAAGAAGATTTGAAAACATTCCCA 4 88 1 ATATAATTTA 0.927032 -101 TGGTTTTGTAATCATCAAAAACAGTTTTAAAAAGCGCAAT 4 145 0 ATATAATTTA 0.927032 -44 TCTTGATTATTTTATAAAAAAATGATACTAATAACGATTA 6 15 0 TTATAAATAA 0.606045 -219 AGCAGGATTTATAATCCAACTTCATTTGAAACCAAACATA 6 85 0 ATATATTTTA 0.629002 -149 AAATATAACTTTACTCAATGAGTTTTTCCAAAAAGTTTTT 9 22 1 TTCTAATTTA 0.812804 -30 GCCATTCAGTTTTGAAAAGAAAAGTTTAAATTAATGGTAA 11 19 1 TTGAAATTTA 0.894099 -164 ACAAGGAAAGTTTAATGAATAATTTTACCATTAATTTAAA 11 43 0 TTAAAATTAA 0.936648 -140 TTTAAAGATCTAGAACTACGAATTTTTTAAAATGAACTTC 11 114 0 TAAAAATTTA 0.637754 -69 AAAAAAGACAATTAAATAACATATTTTAAAGATCTAGAAC 11 138 0 ATAAAATTTA 0.903134 -45 TAATAATCACTTAGTTAAATAATTTTACAAGGTTGTTGTT 13 54 0 TTGTAATTAA 0.873593 -46 TACTAATTGCTTTAATTACTATGCTTTTTATCACTGGAGT 14 236 1 TTAAAATTTA 0.959675 -65 TTTGCATCATTAAATATAATTTAAAGTA 15 6 1 ATATAATTTA 0.927025 -23 ** ** * * *** * Masking position 16 Map Score: 18.7646 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 237 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 ACCCCTCGAATTTTAACAGTTTTTATAATCAAAACAGC 1 205 1 TTAATTTAAA 0.812607 -35 TGAAGTAATTAATCTCTTTAAAATCTTTCAAGA 2 24 0 TTTATTTAAA 0.80671 -23 TTGCTTTGTTTTATTTAGCTGATCAAAAATTAATAATG 3 38 0 TTTTTATAAA 0.8688 -28 TTTTTAAAACTGTTTTTGATGATTACAAAACCATTGAT 4 152 1 TTTTTATAAA 0.862144 -37 ATCACTTGCATCCTTAGAGTGTTAATTATAATTCTTGC 5 12 0 TTTATTTATA 0.923296 -30 CTAGTAATCGTTATTAGTATCATTTTTTT 6 2 1 TTAATATATA 0.679839 -232 TGTGCTGATGTTCTTGATTATTTTATAAAAAAATGATA 6 28 0 TTTGATTAAA 0.634524 -206 CAGGTTCTTTTTTTATTTCTATTTAGTAA 6 215 1 TTATTTTATA 0.922564 -19 TTGAGTAAAGTTATATTTTTATTAAGTAT 9 2 0 TTATTTTATA 0.911879 -50 AATGTTGCTATCATTTGCATATTTAAAA 10 1 0 TTTTTTTAAA 0.943138 -49 TTTAAATTAATGGTAAAATTATTCATTAAACTTTCCTT 11 43 1 TTAATTTATA 0.85043 -140 CTTTCCTTGTTAGTTGTAGTTTTCAATACTGTTTGTAT 11 73 1 TTTGTTTATA 0.921988 -110 TATTTAATTGTCTTTTTTAATTTCATAAATTGT 11 160 1 TTTTATTAAA 0.782116 -23 TACAAGGTTGTTGTTTTTCTAATCAATAAACAAGTGTC 13 31 0 TTTTTATATA 0.903307 -69 AGTATTGCAGTAATATAGATATTAAATAGTAAATTTCT 14 65 1 TTATTTTATA 0.79085 -236 CTTGAGTTTATTATTTCGAAGTTAAATAGAAATTTACT 14 92 0 TTTTATTATA 0.832301 -209 AAAGCGGATCTTCTTTTTGTTTTGAGCATTACTATTGT 14 170 0 TTTTTTTACA 0.815173 -131 CTAATCGTACTAATTGCTTTAATTACTATGCTTTTTAT 14 229 1 TTTGTATATA 0.824664 -72 * *** * ** * ** Masking position 13 Map Score: 16.3779 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 381 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 TAGTGTTGAAAGACAAACATTATTAATTTTTG 3 21 1 AACAAAATTA 0.835282 -45 GTGCTTGTTCATAAAAAAGTAAACGGTTGAAG 4 33 0 AAAAAAGTAA 0.937787 -156 TGATTATTTTATAAAAAAATGATACTAATAAC 6 20 0 AAAAAAATGA 0.850242 -214 CTTCATTTGAAACCAAACATAAATTTAGTGAT 6 74 0 ACCAAAATAA 0.865895 -160 TGGTTACCTGAAACAAAAGTAACCAGCTTCTA 6 148 0 AACAAAGTAA 0.954183 -86 CTAAATAGAAATAAAAAAAGAACCTGTTTTTT 6 209 0 AAAAAAAGAA 0.937787 -25 ATACTTAATAAAAATATAACTTTACTCAA 9 8 1 AAAAAAATAA 0.93668 -44 GAACTTCGAAATACAAACAGTATTGAAAACTA 11 89 0 AACAAAAGTA 0.837856 -94 AAAAATTGGCAAAAAAAGGGGAAATAATTAAA 14 14 0 AAAAAAGGGA 0.854972 -287 AATTTTTGCTAAAAAAATAGAAAATCAGTATT 14 39 1 AAAAAAAGAA 0.937787 -262 AGATGAGAGAAAACAATAGTAATGCTCAAAAC 14 158 1 AACAATGTAA 0.689074 -143 GTAATGCTCAAAACAAAAAGAAGATCCGCTTT 14 176 1 AACAAAAGAA 0.954183 -125 CTAGCAAAAAGTAATCTTAACGGT 14 287 0 ACAAAAGTAA 0.826457 -14 * ***** **** Masking position 6 Map Score: 12.1845 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 109 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 AATCCTAAGGGTATTTAACTAATTATTATA 1 153 1 GTATTTAACT 0.917012 -87 TTGCTTTGTTTTATTTAGCTGATCAAAAAT 3 46 0 TTATTTAGCT 0.95313 -20 GTACAAACGCTTAATTAGCTCCCACATTTT 7 25 0 TTAATTAGCT 0.784682 -31 TTAAAATATGTTATTTAATTGTCTTTTTTA 11 149 1 TTATTTAATT 0.954904 -34 TTTAATTGTCTTTTTTAATTTCATAAATTG 11 162 1 TTTTTTAATT 0.769483 -21 CCTTGTAAAATTATTTAACTAAGTGATTAT 13 62 1 TTATTTAACT 0.976527 -38 TAAGTGATTATTACTTAATTGCACTTTAG 13 81 1 TTACTTAATT 0.849039 -19 TTATTTAATTATTTCCCCTT 14 1 1 TTATTTAATT 0.954904 -300 TAGTAAATTTCTATTTAACTTCGAAATAAT 14 91 1 CTATTTAACT 0.917012 -210 ********** Masking position 5 Map Score: 7.61208 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 62 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 TTTAAAATCTTTCAAGAACTTGGTTTTACA 2 11 0 TTCAAGAACT 0.886758 -36 TATTTAGCTGATCAAAAATTAATAATGTTT 3 35 0 ATCAAAAATT 0.936496 -31 CAAAGGTTTTATGAAGAATTATTTCAAATA 4 67 1 ATGAAGAATT 0.825055 -122 TTTTGTAATCATCAAAAACAGTTTTAAAAA 4 152 0 ATCAAAAACA 0.853697 -37 AGCAAGAATTATAATTAACA 5 1 1 AGCAAGAATT 0.948739 -41 TTATAAAATAATCAAGAACATCAGCACATG 6 38 1 ATCAAGAACA 0.886758 -196 AAAAACTTTTTGGAAAAACTCATTGAGTAA 9 32 0 TGGAAAAACT 0.565297 -20 TATTTTAAAGATCTAGAACTACGAATTTTT 11 127 0 ATCTAGAACT 0.8004 -56 AAAGTAACTGATCAAAAATTTCTTAATAGA 12 11 0 ATCAAAAATT 0.936496 -46 CTATTTTTTTAGCAAAAATTGGCAAAAAAA 14 29 0 AGCAAAAATT 0.932394 -272 CTAGCAAAAAGTAATCTTAACG 14 289 0 AGCAAAAAGT 0.834514 -12 ********** Masking position 5 Map Score: 7.82916 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 190 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ATGGTTCAAGTCCATTTACTTCCACCAATAA 1 66 0 TCCATTACTT 0.850069 -174 TTTTAAAGAGATTAATTACTTCA 2 34 1 ATTATTACTT 0.901534 -13 TCAAACTTCAACCGTTTACTTTTTTATGAAC 4 28 1 ACCGTTACTT 0.893653 -161 TTATCACTTGCATCCTTAGAGTG 5 29 0 ATCATTGCAT 0.879251 -13 CAATGTTGCTATCATTTGCATATTTAAAA 10 9 0 ATCATTGCAT 0.879251 -41 GAAATTTTTGATCAGTTACTTTTACCTAGAT 12 19 1 ATCATTACTT 0.965441 -38 TTAAGTAATAATCACTTAGTTAAATAATTTT 13 68 0 ATCATTAGTT 0.802335 -32 TTCTAATCGTACTAATTGCTTTAATTACTAT 14 227 1 ACTATTGCTT 0.906741 -74 AACGGTTGCGACTAATTACTCCAGTGATAAA 14 262 0 ACTATTACTC 0.733623 -39 **** ****** Masking position 6 Map Score: 1.84989 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 173 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 AATTATTATAACAATTTTAATTTAACCAAAA 1 173 1 AAATTTTAAT 0.938251 -67 AAGTTCTTGAAAGATTTTAAAGAGATTAATT 2 20 1 AGATTTTAAA 0.705593 -27 ATAAATTTAATAGTGTTGAAA 3 1 1 AAAATTTAAT 0.89948 -65 ATCATCAAAAACAGTTTTAAAAAGCGCAATT 4 144 0 AAGTTTTAAA 0.705593 -45 AGCAAGAATTATAATTAACACTCTA 5 5 1 AAATTATAAT 0.617879 -37 GAAACCAAACATAAATTTAGTGATAAAGATC 6 67 0 AAAATTTAGT 0.676634 -167 ACATTTTTGGAAAATTTTAAA 7 1 0 AAATTTTAAA 0.938254 -55 TAATAAAAATATAACTTTACTCAATGAGTTT 9 16 1 AAACTTTACT 0.768528 -36 TTTTGAAAAGAAAAGTTTAAATTAATGGTAA 11 28 1 AAAGTTTAAA 0.801428 -155 AGTTTAATGAATAATTTTACCATTAATTTAA 11 44 0 AAATTTTACC 0.793662 -139 TTTTACCTAGATAAATTTAAAGTTTATTT 12 38 1 AAAATTTAAA 0.899588 -19 ACTTAGTTAAATAATTTTACAAGGTTGTTGT 13 55 0 AAATTTTACA 0.925929 -45 GAAGTTAAATAGAAATTTACTATTTAATATC 14 82 0 AAAATTTACT 0.880443 -219 * ********* Masking position 9 Map Score: 6.79987 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 141 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 AAAGTAAACGGTTGAAGTTTGATGTATTAG 4 20 0 GTTGAAGTTT 0.95717 -169 AAGATCATGTGCTGATGTTCTTGATTATTT 6 43 0 GCTGATGTTC 0.915737 -191 TTCCTTGTTAGTTGTAGTTTTCAATACTGT 11 75 1 GTTGTAGTTT 0.95717 -108 TAAAAACAAAGCTGTAGTTGACACTTGTTT 13 12 1 GCTGTAGTTG 0.952382 -88 ATTTTACAAGGTTGTTGTTTTTCTAATCAA 13 43 0 GTTGTTGTTT 0.95717 -57 ACAATCTTCTGTTGATCTTGAGTTTATTAT 14 116 0 GTTGATCTTG 0.846895 -185 ********** Masking position 3 Map Score: 0.901644 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 112 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 CTCAACTGATAGAGCACCTGATTTGCACTCAGGAG 1 20 0 AGAACGTTTG 0.980946 -220 TACCCCTCGAATTTTAACAGTTTTTATAATCAAAA 1 204 1 ATTACGTTTT 0.786103 -36 AAAATTAGCTGTTTTGATTATAAAAA 1 224 0 AAAACGTTTG 0.977076 -16 TTCTGCTAAATCAATGGTTTTGTAATCATCAA 4 167 0 AAAATGTTTG 0.806926 -22 GCATGATTACAATAAAGCAGGATTTATAATCCAAC 6 105 0 AATACGATTT 0.782458 -129 AGAAATAAAAAAAGAACCTGTTTTTTTCAGGTTCT 6 200 0 AAAACGTTTT 0.95593 -34 GAACTTCGAAATACAAACAGTATTGAAAACTACAA 11 86 0 ATAACGATTG 0.922995 -97 CTAAAAAAATAGAAAATCAGTATTGCAGTAATATA 14 47 1 AGAACGATTG 0.964293 -254 CAAAACAAAAAGAAGATCCGCTTTTTAGCTTTGGG 14 184 1 AGAACGTTTT 0.96323 -117 *** * * * **** Masking position 6 Map Score: 4.9681 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 73 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 GTTCTTGAAAGATTTTAAAGAGATTAATTA 2 22 1 GATTTTAAAG 0.848088 -25 TGCTTTGTTTTATTTAGCTGATCAAAAATT 3 45 0 TATTTAGCTG 0.772335 -21 CAAAACCATTGATTTAGCAGAA 4 177 1 GATTTAGCAG 0.951768 -12 TCATGCTTTAGATTTAGAAGCTGGTTACTT 6 134 1 GATTTAGAAG 0.96702 -100 ATACTGTTTGTATTTCGAAGTTCATTTTAA 11 98 1 TATTTCGAAG 0.963255 -85 TTAAATAACATATTTTAAAGATCTAGAACT 11 137 0 TATTTTAAAG 0.822161 -46 TTGAGTTTATTATTTCGAAGTTAAATAGAA 14 99 0 TATTTCGAAG 0.963255 -202 ********** Masking position 2 Map Score: 2.76856 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 42 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 TTATCACTTGCATCCTTAGAGTGTTAATTA 5 22 0 GCATCCTTAA 0.96798 -20 TAAATCTAAAGCATGATTACAATAAAGCAGG 6 119 0 GCATGATTAA 0.950147 -115 GCAAATGATAGCAACATTGAACGTGCTGAAA 10 21 1 GCAACATTGA 0.901849 -29 TTAGCTTTGGGCATCATTATTCTAATCGTAC 14 208 1 GCATCATTAT 0.953264 -93 TTTGCATCATTAAATATAATTTAA 15 4 1 GCATCATTAA 0.985317 -25 ********* * Masking position 7 Map Score: 0.10325 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 19 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 ********** No masking Map Score: 1.45904e-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: 1.45904e-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: 1.45904e-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