AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_mgen_reg_300.orf -o00051_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 MG022 29 DNA-directed RNA polymerase, subunit delta (rpoE) #7 MG062 300 PTS system, fructose-specific IIABC component (fruA) #8 MG063 94 1-phosphofructokinase (fruK) #9 MG069 300 PTS system, glucose-specific IIABC component (ptsG) #10 MG210.1 200 conserved hypothetical protein #11 MG211 189 conserved hypothetical protein #12 MG431 59 triosephosphate isomerase (tpiA) #13 MG432 85 conserved hypothetical protein Motif number 1 AATTGTTATAATAATTAGTTAAATACCCTTAGG 1 156 0 ATAATTATAA 0.767494 -84 ACTAATTATTATAACAATTTTAATTTAACCAAA 1 170 1 ATAACAATAA 0.867151 -70 TTTGATTATAAAAACTGTTAAAATTCGAGGGGT 1 205 0 AAAACTGTAA 0.931461 -35 CTCAAAAAACTAATACATCAAACTTCAA 4 6 1 AAAACTATAT 0.84392 -183 GGTTTTATGAAGAATTATTTCAAATAGATTATT 4 71 1 AGAATTATAA 0.872084 -118 GTAATCATCAAAAACAGTTTTAAAAAGCGCAAT 4 145 0 AAAACAGTAA 0.89457 -44 TACAGCTTTTAAAATTAGTCTAATGTAAATTCT 7 17 0 AAAATTATAA 0.934516 -284 ATTGTTTTTTAGAACAAACTGAATCAAAGAATT 7 54 1 AGAACAACAA 0.747056 -247 TTAACAATGAAAGACAATTTCAAATTCTTTGAT 7 76 0 AAGACAATAA 0.729561 -225 ATTTAACAACAAAATTGAATAAAAATAAAAAAC 7 113 1 AAAATTGAAA 0.465475 -188 TTGCATATTTATAATAAATTTAACAACAAACTG 7 262 0 ATAATAATAA 0.673299 -39 TAAAATTCCAAAAACAACTAAAAGAGCATATGT 9 27 0 AAAACAATAA 0.965776 -274 TAGTCCAATTAGAACTAATAAAATTCCAAAAAC 9 45 0 AGAACTATAA 0.955738 -256 TTTCACTTAAAGAACAAAAGAAAGGTCAAATTA 9 103 1 AGAACAAAAA 0.732329 -198 ATTGCAAGCAAAAATAAAACTAATTTGTTGTTT 9 200 0 AAAATAAAAA 0.643901 -101 TAGCATTAAAAAAACTATTGCAAGCAAAAATAA 9 216 0 AAAACTATAA 0.978354 -85 TTTAAAACTACTAAATTTTATTAACC 9 285 0 AAAACTATAT 0.84392 -16 AGTTAGTTTAAAAACTAGTAAAAAAGTGTTAAT 10 67 0 AAAACTATAA 0.978354 -134 ATTAGTAAAGAAAACTACCAGAAATTAAACTAG 10 115 0 AAAACTACAA 0.908274 -86 ATGGTTTTTGAAAACTTATAAAATCTTTCAT 12 39 1 AAAACTTTAA 0.773785 -21 ATTAATTACCAAAATTATTAAAATAATTGTTCT 13 58 1 AAAATTATAA 0.934516 -28 ******* * ** Masking position 4 Map Score: 23.5173 Number of sites scoring better than the average of aligned sites = 576 Number in coding regions = 498 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 AATTATTATAACAATTTTAATTTAACCAAA 1 173 1 ACAATTTTAA 0.754812 -67 TTGTCTTTCAACACTATTAAATTTAT 3 7 0 ACACTATTAA 0.736322 -59 TGAAAGACAAACATTATTAATTTTTGATCA 3 27 1 ACATTATTAA 0.950355 -39 TCAACCGTTTACTTTTTTATGAACAAGCAC 4 35 1 ACTTTTTTAT 0.782244 -154 ATCATCAAAAACAGTTTTAAAAAGCGCAAT 4 145 0 ACAGTTTTAA 0.820232 -44 TTTGTTGTTAAATTTATTATAAATATGCAA 7 265 1 AATTTATTAT 0.454871 -36 TCTTTAAGTGAAATTTTTAAAGCTCAAAAT 9 86 0 AAATTTTTAA 0.922307 -215 TCTAGGAACTTCATTTTTAAGTGAGTTATT 9 153 0 TCATTTTTAA 0.834688 -148 TAACTAACAAAAATTATTAAGGAGTATTAA 10 42 1 AAATTATTAA 0.879015 -159 GAGTATTAACACTTTTTTACTAGTTTTTAA 10 63 1 ACTTTTTTAC 0.847483 -138 TTTTAAACTAACTTTTTTAAGTGTAATCCT 10 87 1 ACTTTTTTAA 0.950356 -114 TCTAACTTTTAATTTTTTACAAGTAGCTAT 10 146 0 AATTTTTTAC 0.678344 -55 CTCTAAATCATCATTTTTAACTTCAATCTT 11 16 0 TCATTTTTAA 0.834688 -174 ATCCTTTTAAACTTTTTTAAAGCTAGCTCT 11 42 0 ACTTTTTTAA 0.950356 -148 AGTAAATAAGAAATTATTAATTACCAAAAT 13 43 1 AAATTATTAA 0.879015 -43 TTAATTACCAAAATTATTAAAATAATTGTT 13 59 1 AAATTATTAA 0.879015 -27 ********** Masking position 5 Map Score: 15.9052 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 194 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 TTTAACAGTTTTTATAATCAAAACAGCTAATT 1 216 1 TTTAATCAAA 0.898969 -24 CGTTTACTTTTTTATGAACAAGCACTACAAAG 4 40 1 TTTAAACAAG 0.666732 -149 CTACAAAGGTTTTATGAAGAATTATTTCAAAT 4 64 1 TTTAAAGAAT 0.600743 -125 CCCATTAAAGATAAGAATCAAATTGCGCTTTT 4 124 1 ATAAATCAAA 0.810657 -65 CAATGGTTTTGTAATCATCAAAAACAGTTTTA 4 156 0 GTAAATCAAA 0.870671 -33 AATTAACACTCTAAGGATGCAAGTGATAA 5 23 1 CTAAATGCAA 0.506241 -19 TCAGTTTGTTCTAAAAAACAATTAGCTACAGC 7 44 0 CTAAAACAAT 0.606785 -257 TTAAATGCTGTTAACAATGAAAGACAATTTCA 7 87 0 TTAAATGAAA 0.914326 -214 GTTAACAGCATTTAACAACAAAATTGAATAAA 7 104 1 TTTAAACAAA 0.906409 -197 GCTTCCGCCATTAAATATCCAACAGACCATCA 7 152 0 TTAAATCCAA 0.902447 -149 TTATAATAAATTTAACAACAAACTGGGAGCGT 7 255 0 TTTAAACAAA 0.906409 -46 TAAATTTATTATAAATATGCAACTAATTAGCG 7 273 1 ATAAATGCAA 0.487118 -28 TTAAATCAACATAATAATCAATTGCGCAAGCG 8 14 0 ATAAATCAAT 0.567729 -81 TTATGTTGATTTAAACAAGCAAAAAAATAGTG 8 32 1 TTAAAAGCAA 0.835898 -63 AGTGAAATTTTTAAAGCTCAAAATAAAAATCC 9 78 0 TTAACTCAAA 0.637308 -223 AAAATTTCACTTAAAGAACAAAAGAAAGGTCA 9 99 1 TTAAAACAAA 0.958256 -202 AATAACTCACTTAAAAATGAAGTTCCTAGAGG 9 153 1 TTAAATGAAG 0.687788 -148 ACTACTAAATTTTATTAACCAAACAGCTTAGG 9 273 0 TTTAAACCAA 0.809281 -28 AATTCACTAATTAACTAACAAAAATTATTAAG 10 31 1 TTAAAACAAA 0.958263 -170 CAAGTAGCTATTAGTAAAGAAAACTACCAGAA 10 125 0 TTAGAAGAAA 0.491731 -76 CTTAATGATCAATTAGTTGGAAA 12 2 1 TTAAATCAAT 0.866157 -58 TAATAAGATAGTAAATAAGAAATTATTAATTA 13 34 1 GTAAAAGAAA 0.787538 -52 TAAGAAATTATTAATTACCAAAATTATTAAAA 13 49 1 TTAAACCAAA 0.783507 -37 AGTTAAGAACAATTATTTTAATA 13 73 0 GTTAAACAAT 0.486975 -13 **** ****** Masking position 2 Map Score: 18.739 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 432 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 CCTGATTTGCACTCAGGAGGTTGAGGGT 1 7 0 ACTCAAGGTT 0.835038 -233 TCAACTGATAGAGCACCTGATTTGCACTCAGG 1 22 0 GAGCATGATT 0.845244 -218 TGGGGATGTAGCTCAACTGATAGAGCACCTGA 1 34 0 GCTCATGATA 0.892022 -206 TGGAAGTATAGCTCAGTTGGTTAGAGCACACC 1 116 0 GCTCATGGTT 0.990558 -124 CTGGGAGCGTACTCAAGTGGTTAAGAGGACAC 7 233 0 ACTCATGGTT 0.946757 -68 TTACGCTTGCGCAATTGATTATTATGTTGA 8 9 1 GCGCATGATT 0.969823 -86 AACAACATATGCTCTTTTAGTTGTTTTTGGAA 9 23 1 GCTCTTAGTT 0.807206 -278 GCATCCCTTTGCGCAAGTGGTATTCATGGCGT 11 99 0 GCGCATGGTA 0.969474 -91 CACAGAAAAAGCGCAGGAAGTTTCGCAGTTTA 11 155 1 GCGCAAAGTT 0.899612 -35 CTTAATGATCAATTAGTTGGAAAAGAAA 12 7 1 GATCATAGTT 0.83721 -53 ***** ***** Masking position 11 Map Score: 7.06407 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 41 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 ATTAATAATGTTTGTCTTTCAACACTATTA 3 18 0 TTTGTCTTTC 0.725254 -48 TTGCTTTGTTTTATTTAGCTGATC 3 52 0 TTTGTTTTAT 0.787612 -14 GTTTGATGTATTAGTTTTTTGAG 4 4 0 TTAGTTTTTT 0.88942 -185 GCTGTAGCTAATTGTTTTTTAGAACAAACT 7 44 1 ATTGTTTTTT 0.851034 -257 AGAATTTGAAATTGTCTTTCATTGTTAACA 7 81 1 ATTGTCTTTC 0.396304 -220 TTTATTCAATTTTGTTGTTAAATGCTGTTA 7 106 0 TTTGTTGTTA 0.835794 -195 ACCATCAGGGTCTGTTTTTTATTTTTATTC 7 129 0 TCTGTTTTTT 0.770173 -172 ACGCTCCCAGTTTGTTGTTAAATTTATTAT 7 255 1 TTTGTTGTTA 0.835794 -46 AATTGATTATTATGTTGATTTAAACAAGCA 8 23 1 TATGTTGATT 0.270113 -72 TAAAAGAGCATATGTTGTTTGCATGCAACA 9 12 0 TATGTTGTTT 0.812209 -289 ATATGCTCTTTTAGTTGTTTTTGGAATTTT 9 29 1 TTAGTTGTTT 0.897175 -272 TGACCTTTCTTTTGTTCTTTAAGTGAAATT 9 101 0 TTTGTTCTTT 0.827315 -200 ATAAAACTAATTTGTTGTTTCTTTTTCATC 9 190 0 TTTGTTGTTT 0.961421 -111 AAACAACAAATTAGTTTTATTTTTGCTTGC 9 200 1 TTAGTTTTAT 0.564911 -101 TTTGCTTGCAATAGTTTTTTTAATGCTAGG 9 221 1 ATAGTTTTTT 0.666692 -80 TGTGCTATCTTTTGTTTTTCTCTTAACCGC 11 129 0 TTTGTTTTTC 0.913583 -61 ********** Masking position 5 Map Score: 12.6551 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 545 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 ATGGGGATGTAGCTCAACTGATAGAGCACC 1 37 0 AGCTCAACTG 0.964296 -203 TTGGAAGTATAGCTCAGTTGGTTAGAGCAC 1 119 0 AGCTCAGTTG 0.899448 -121 GAGGACACCCTGCTAAGGTGTTAGATCGTT 7 211 0 TGCTAAGGTG 0.951352 -90 ACTGGGAGCGTACTCAAGTGGTTAAGAGGA 7 236 0 TACTCAAGTG 0.814028 -65 TTACGCTTGCGCAATTGATTATTATGT 8 8 1 TGCGCAATTG 0.89478 -87 TTGTTTCCCTTCCTAAGCTGTTTGGTTAAT 9 262 1 TCCTAAGCTG 0.809569 -39 CATGGCGTTGTGCTAACCTGCGTACTTCCA 11 77 0 TGCTAACCTG 0.9055 -113 CGCATCCCTTTGCGCAAGTGGTATTCATGG 11 102 0 TGCGCAAGTG 0.950398 -88 CTTAATGGCTAGCTAAACTGCGAAACTTCC 11 170 0 AGCTAAACTG 0.932187 -20 ********** Masking position 6 Map Score: 4.24018 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 22 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TTTTGGTTAAATTAAAATTGTTATAATAAT 1 174 0 ATTAAAATTG 0.8359 -66 TATAAAAACTGTTAAAATTCGAGGGGTATT 1 202 0 GTTAAAATTC 0.937516 -38 TAGAGTGTTAATTATAATTCTTGCT 5 6 0 ATTATAATTC 0.826038 -36 AAATCAATAAAATTCTAATACTACT 6 15 0 AATAAAATTC 0.963632 -15 AATTAGAACTAATAAAATTCCAAAAACAAC 9 42 0 AATAAAATTC 0.963632 -259 TAAAGCTCAAAATAAAAATCCTAGTCCAAT 9 69 0 AATAAAAATC 0.826035 -232 CTGTTTGGTTAATAAAATTTAGTAGTTTTA 9 279 1 AATAAAATTT 0.774616 -22 TGTATATTCAGTTAAAATTCACTAATTAAC 10 16 1 GTTAAAATTC 0.937516 -185 ********** Masking position 6 Map Score: 5.89155 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 24 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 CTTCCACCAATAATGGGGATGTAGCTCAAC 1 49 0 TAATGGGGAT 0.771488 -191 TTGGTGGAAGTAAATGGACTTGAACCATCG 1 69 1 TAAATGGACT 0.830339 -171 AGCATAATCCTAAGGGTATTTAACTAATTA 1 148 1 TAAGGGTATT 0.79588 -92 TTCTTATCTTTAATGGGAATGTTTTCAAAT 4 111 0 TAATGGGAAT 0.941823 -78 TACCTGGTGGTAAGGGGATTAATGTTGCTA 8 70 1 TAAGGGGATT 0.944589 -25 TTATTAGTTCTAATTGGACTAGGATTTTTA 9 57 1 TAATTGGACT 0.941527 -244 TTTTGTTCTTTAAGTGAAATTTTTAAAGCT 9 92 0 TAAGTGAAAT 0.721219 -209 ATGCTAGGAATAGGTGGACTTGTTTCCCTT 9 243 1 TAGGTGGACT 0.868379 -58 CTAACTTTTTTAAGTGTAATCCTAGTTTAA 10 94 1 TAAGTGTAAT 0.820205 -107 AAGTTAGAATTAATGGCACTATTTAGTATA 10 168 1 TAATGGCACT 0.83155 -33 ********** Masking position 2 Map Score: 2.54796 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 54 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 CATCCCCATTATTGGTGGAAGTAAATGGACTT 1 58 1 ATGTGGAAGT 0.980508 -182 GGGTGAGGTCGATGGTTCAAGTCCATTTACTT 1 76 0 GAGTTCAAGT 0.823981 -164 CCTTAGGATTATGCTTGGAAGTATAGCTCAGT 1 131 0 ATCTGGAAGT 0.920216 -109 TAAAAAAGTAAACGGTTGAAGTTTGATGTATT 4 22 0 AAGTTGAAGT 0.951604 -167 TTAACACTCTAAGGATGCAAGTGATAA 5 25 1 AAGTGCAAGT 0.9468 -17 TTTTAAGTGAGTTATTGGAAGTCAAATCATTA 9 137 0 GTATGGAAGT 0.902286 -164 TGCCTAAGATTGAAGTTAAAAATGAT 11 5 1 TAGTTGAAGT 0.829086 -185 TTAAAAGGATATCACTGGAAGTACGCAGGTTA 11 62 1 ATATGGAAGT 0.932076 -128 ** * ******* Masking position 9 Map Score: 1.02496 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 29 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ********** No masking Map Score: 3.91042e-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 CTGTTTTGATTATAAAAACTGTTAAAATTC 1 212 0 TATAAAAACT 0.603056 -28 AATTAATCTCTTTAAAATCTTTCAAGAACT 2 21 0 TTTAAAATCT 0.959248 -26 ATGGGAATGTTTTCAAATCTTCTTAAATAA 4 99 0 TTTCAAATCT 0.815934 -90 ATTAGTCTAATGTAAATTCTGTCTTA 7 7 0 TGTAAATTCT 0.62815 -294 TTAGACTAATTTTAAAAGCTGTAGCTAATT 7 27 1 TTTAAAAGCT 0.956547 -274 GAAAGACAATTTCAAATTCTTTGATTCAGT 7 71 0 TTCAAATTCT 0.589394 -230 AAAATAGTGTTTTAATACCTGGTGGTAAGG 8 55 1 TTTAATACCT 0.64661 -40 TAAGTGAAATTTTTAAAGCTCAAAATAAAA 9 82 0 TTTTAAAGCT 0.876044 -219 GCAATAGTTTTTTTAATGCTAGGAATAGGT 9 228 1 TTTTAATGCT 0.747121 -73 AAAAAGTTAGTTTAAAAACTAGTAAAAAAG 10 74 0 TTTAAAAACT 0.881494 -127 GTAATCCTAGTTTAATTTCTGGTAGTTTTC 10 109 1 TTTAATTTCT 0.742257 -92 TTTTAAACTTTTTTAAAGCTAGCTCTAAAT 11 38 0 TTTTAAAGCT 0.876044 -152 TTTGAAAACTTATAAAATCTTTCAT 12 45 1 TATAAAATCT 0.827814 -15 TAATTTCTTATTTACTATCTTATTAGTAAT 13 29 0 TTTACTATCT 0.501224 -57 ********** Masking position 1 Map Score: 7.67299 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 240 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 ********** No masking Map Score: 3.91042e-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: 3.91042e-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 TTTATAATCAAAACAGCTAATTTT 1 226 1 AAACGCAATT 0.971871 -14 ACAGTTTTAAAAAGCGCAATTTGATTCTTATC 4 133 0 AAAGGCATTT 0.8649 -56 CTAAAGCGCTAATTAGTTGCATAT 7 287 0 AAAGGCAATT 0.977116 -14 TGAAATTTTTAAAGCTCAAAATAAAAATCCTA 9 76 0 AAAGTCAAAT 0.916509 -225 AGAACAAAAGAAAGGTCAAATTACTAATGATT 9 113 1 AAAGTCAATT 0.954368 -188 GATGAAAAAGAAACAACAAATTAGTTTTATTT 9 190 1 AAACACAATT 0.921811 -111 TTTAAAACTACTAAATTTTATTAACC 9 285 0 AAACACAAAT 0.860819 -16 TAAAAAATTAAAAGTTAGAATTAATGGCACTA 10 157 1 AAAGTAAATT 0.672289 -44 ATGGCTAGCTAAACTGCGAAACTTCCTGCGCT 11 164 0 AAACGCAAAC 0.810483 -26 **** ** **** Masking position 9 Map Score: 3.46119 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 56 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 ********** No masking Map Score: 3.91042e-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