AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_mgen_reg_100.orf -o00051_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 MG018 188 ATP-dependent RNA helicase, putative #2 MG019 41 heat shock protein (dnaJ) #3 MG022 29 DNA-directed RNA polymerase, subunit delta (rpoE) #4 MG062 300 PTS system, fructose-specific IIABC component (fruA) #5 MG063 94 1-phosphofructokinase (fruK) #6 MG069 300 PTS system, glucose-specific IIABC component (ptsG) #7 MG211 189 conserved hypothetical protein #8 MG431 59 triosephosphate isomerase (tpiA) #9 MG432 85 conserved hypothetical protein Motif number 1 AAAAGCGCAATTTGATTCTTATCTTTAATGG 1 125 0 TTTGATCTTA 0.905554 -64 TAAAACTGTTTTTGATGATTACAAAACCATT 1 156 1 TTTGATATTA 0.934422 -33 TTATCACTTGCATCCTTAGAGTGTTAAT 2 24 0 TTGCATCTTA 0.657057 -18 GCTGTAGCTAATTGTTTTTTAGAACAAACTG 4 44 1 ATTGTTTTTA 0.905314 -257 TTTATTCAATTTTGTTGTTAAATGCTGTTAA 4 105 0 TTTGTTTTAA 0.905314 -196 ACCATCAGGGTCTGTTTTTTATTTTTATTCA 4 128 0 TCTGTTTTTA 0.794283 -173 TGATGGTCTGTTGGATATTTAATGGCGGAAG 4 152 1 TTGGATTTTA 0.969211 -149 ACGCTCCCAGTTTGTTGTTAAATTTATTATA 4 255 1 TTTGTTTTAA 0.905314 -46 CGCTAATTAGTTGCATATTTATAATAAATTT 4 274 0 TTGCATTTTA 0.8847 -27 CGCTTGCGCAATTGATTATTATGTTGATTTA 5 14 1 ATTGATATTA 0.780117 -81 CACTATTTTTTTGCTTGTTTAAATCAACATA 5 33 0 TTGCTTTTTA 0.8847 -62 TTAGTTGTTTTTGGAATTTTATTAGTTCTAA 6 39 1 TTGGAATTTA 0.681081 -262 CTAATTGGACTAGGATTTTTATTTTGAGCTT 6 66 1 TAGGATTTTA 0.681081 -235 GGATTTTTATTTTGAGCTTTAAAAATTTCAC 6 78 1 TTTGAGTTTA 0.794283 -223 TGACCTTTCTTTTGTTCTTTAAGTGAAATTT 6 100 0 TTTGTTTTTA 0.974619 -201 ATAAAACTAATTTGTTGTTTCTTTTTCATCA 6 189 0 TTTGTTTTTC 0.78591 -112 CCTAAGCTGTTTGGTTAATAAAATTTAGTAG 6 273 1 TTGGTTATAA 0.744145 -28 TTTCCAACTAATTGATCATTAAG 8 3 0 ATTGATATTA 0.780117 -57 TAATTAATAATTTCTTATTTACTATCTTATT 9 35 0 TTTCTTTTTA 0.903474 -51 TTTTAATAATTTTGGTAATTAATAATTTCTT 9 50 0 TTTGGTATTA 0.728511 -36 TATTAAAATAATTGTTCTTAACT 9 73 1 ATTGTTTTAA 0.704198 -13 ****** **** Masking position 9 Map Score: 20.3523 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 553 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 CTCAAAAAACTAATACATCAAACTT 1 6 1 AAAACTAATA 0.94187 -183 AATTCTTCATAAAACCTTTGTAGTGCTTGT 1 57 0 AAAACCTTTG 0.680169 -132 GGTTTTATGAAGAATTATTTCAAATAGATT 1 71 1 AGAATTATTT 0.491423 -118 TGCGCTTTTTAAAACTGTTTTTGATGATTA 1 147 1 AAAACTGTTT 0.783184 -42 TGATGATTACAAAACCATTGATTTAGCAGA 1 168 1 AAAACCATTG 0.924555 -21 TTTGTTCTAAAAAACAATTAGCTACAGCTT 4 42 0 AAAACAATTA 0.92561 -259 CAGGTATTAAAACACTATTTTTTTGCTTGT 5 46 0 AACACTATTT 0.758501 -49 TAAAATTCCAAAAACAACTAAAAGAGCATA 6 30 0 AAAACAACTA 0.811766 -271 TAGTCCAATTAGAACTAATAAAATTCCAAA 6 48 0 AGAACTAATA 0.863684 -253 AAGCAAAAATAAAACTAATTTGTTGTTTCT 6 198 0 AAAACTAATT 0.91192 -103 TAGCATTAAAAAAACTATTGCAAGCAAAAA 6 219 0 AAAACTATTG 0.960435 -82 TTTAAAACTACTAAATTTTATTA 6 288 0 AAAACTACTA 0.930713 -13 TAAGTTTTCAAAAACCATTTTCTTTTCCAA 8 27 0 AAAACCATTT 0.92591 -33 ATGGTTTTTGAAAACTTATAAAATCTTTCA 8 39 1 AAAACTTATA 0.737673 -21 ATTAATTACCAAAATTATTAAAATAATTGT 9 58 1 AAAATTATTA 0.794535 -28 AGTTAAGAACAATTATTTTAATAAT 9 71 0 AGAACAATTA 0.829522 -15 ********** Masking position 4 Map Score: 13.3234 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 499 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 AAACGGTTGAAGTTTGATGTATTAGTTTTT 1 15 0 AGTTTGATGT 0.909207 -174 TCTTTGATTCAGTTTGTTCTAAAAAACAAT 4 54 0 AGTTTGTTCT 0.959315 -247 TTTTTATTCAATTTTGTTGTTAAATGCTGT 4 108 0 ATTTTGTTGT 0.972631 -193 GTACGCTCCCAGTTTGTTGTTAAATTTATT 4 253 1 AGTTTGTTGT 0.982419 -48 ACTAAAAGAGCATATGTTGTTTGCATGCAA 6 14 0 CATATGTTGT 0.813308 -287 TTTGACCTTTCTTTTGTTCTTTAAGTGAAA 6 103 0 CTTTTGTTCT 0.936299 -198 AAATAAAACTAATTTGTTGTTTCTTTTTCA 6 192 0 AATTTGTTGT 0.961242 -109 TCTGTGCTATCTTTTGTTTTTCTCTTAACC 7 131 0 CTTTTGTTTT 0.843474 -59 ********** Masking position 5 Map Score: 7.57279 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 75 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 ACCGTTTACTTTTTTATGAACAAGCACTACAAA 1 38 1 TTTTTAACAA 0.78881 -151 TAGCTAATTGTTTTTTAGAACAAACTGAATCAA 4 48 1 TTTTAAACAA 0.837381 -253 TTTGAAATTGTCTTTCATTGTTAACAGCATTTA 4 85 1 TTTTATGTTA 0.541317 -216 GTCTGTTTTTTATTTTTATTCAATTTTGTTGTT 4 117 0 TTTTTTTCAA 0.830126 -184 ATTAAAACACTATTTTTTTGCTTGTTTAAATCA 5 38 0 TTTTTTGCTT 0.790259 -57 GAGCATATGTTGTTTGCATGCAACAT 6 4 0 TTTTCTGCAA 0.951233 -297 TTTCTTTTGTTCTTTAAGTGAAATTTTTAAAGC 6 93 0 TTTTATGAAA 0.541316 -208 ATTTGTTGTTTCTTTTTCATCAACTCCCTCTAG 6 178 0 TTTTTATCAA 0.793256 -123 ATTAGTTTTATTTTTGCTTGCAATAGTTTTTTT 6 209 1 TTTTCTGCAA 0.951233 -92 TTGCAATAGTTTTTTTAATGCTAGGAATAGGTG 6 226 1 TTTTATGCTA 0.954247 -75 TAAATCATCATTTTTAACTTCAATCTTAGGCA 7 10 0 TTTTATTCAA 0.870588 -180 CCTTTTAAACTTTTTTAAAGCTAGCTCTAAATC 7 37 0 TTTTAAGCTA 0.942378 -153 CTTCCTGCGCTTTTTCTGTGCTATCTTTTGTTT 7 142 0 TTTTTTGCTA 0.938082 -48 AAAACCATTTTCTTTTCCAACTAATTGATCATT 8 14 0 TTTTCAACTA 0.831639 -46 AAGAAAATGGTTTTTGAAAACTTATAAAATCTT 8 33 1 TTTTAAACTT 0.567728 -27 AATAATTTCTTATTTACTATCTTATTAGTAATA 9 28 0 TTTTCATCTT 0.551263 -58 * *** * ***** Masking position 5 Map Score: 12.0406 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 344 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 AAAACCTTTGTAGTGCTTGTTCATAAAAAA 1 47 0 TAGTGCTTGT 0.834511 -142 TAATAATCAATTGCGCAAGCGTAA 5 5 0 TTGCGCAAGC 0.949516 -90 AACACTATTTTTTTGCTTGTTTAAATCAAC 5 36 0 TTTTGCTTGT 0.795743 -59 ATGTTGCATGCAAACAACATA 6 2 1 TGTTGCATGC 0.775199 -299 TTAAAAAAACTATTGCAAGCAAAAATAAAA 6 214 0 TATTGCAAGC 0.944132 -87 CAAGTCCACCTATTCCTAGCATTAAAAAAA 6 235 0 TATTCCTAGC 0.762181 -66 AATGATGATTTAGAGCTAGCTTTAAAAAAG 7 31 1 TAGAGCTAGC 0.935271 -159 ATTCATGGCGTTGTGCTAACCTGCGTACTT 7 80 0 TTGTGCTAAC 0.809448 -110 CCGCATCCCTTTGCGCAAGTGGTATTCATG 7 103 0 TTGCGCAAGT 0.841443 -87 AGTTTCGCAGTTTAGCTAGCCATTAAG 7 173 1 TTTAGCTAGC 0.917742 -17 ********** Masking position 1 Map Score: 3.89054 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 94 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 GTTTTAAAAAGCGCAATTTGATTCTTATCT 1 132 0 GCGCAATTTG 0.919614 -57 ATATTTAATGGCGGAAGCGGTGGGATTCGA 4 166 1 GCGGAAGCGG 0.989533 -135 CTGGGAGCGTACTCAAGTGGTTAAGAGGAC 4 235 0 ACTCAAGTGG 0.919578 -66 ATAATCAATTGCGCAAGCGTAA 5 3 0 GCGCAAGCGT 0.975105 -92 GCATCCCTTTGCGCAAGTGGTATTCATGGC 7 101 0 GCGCAAGTGG 0.996694 -89 ********** Masking position 5 Map Score: 2.31025 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 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 7 TATGAAGAATTATTTCAAATAGATTATTTA 1 76 1 TATTTCAAAT 0.902426 -113 CTTAGAGTGTTAATTATAATTCTTGCT 2 8 0 TAATTATAAT 0.678441 -34 AAATCAATAAAATTCTAATACTACTTTTC 3 11 0 AAATTCTAAT 0.896873 -19 AATGAAAGACAATTTCAAATTCTTTGATTC 4 74 0 AATTTCAAAT 0.88239 -227 ATTAGTTGCATATTTATAATAAATTTAACA 4 270 0 TATTTATAAT 0.852141 -31 GGAATTTTATTAGTTCTAATTGGACTAGGA 6 51 1 TAGTTCTAAT 0.900057 -250 AGAAAGGTCAAATTACTAATGATTTGACTT 6 121 1 AATTACTAAT 0.882451 -180 CTAAGCTTAATATTACTAATAAGATAGTAA 9 18 1 TATTACTAAT 0.902428 -68 GGTAATTAATAATTTCTTATTTACTATCTT 9 38 0 AATTTCTTAT 0.789249 -48 ********** Masking position 4 Map Score: 5.15824 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 91 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TTGAAATAATTCTTCATAAAACCTTTGTAG 1 64 0 TCTTCATAAA 0.736846 -125 TGTTTTCAAATCTTCTTAAATAATCTATTT 1 92 0 TCTTCTTAAA 0.918595 -97 TTGAAAACATTCCCATTAAAGATAAGAATC 1 113 1 TCCCATTAAA 0.86054 -76 TAGCAGGGTGTCCTCTTAACCACTTGAGTA 4 226 1 TCCTCTTAAC 0.983171 -75 GCAACATTAATCCCCTTACCACCAGGTATT 5 68 0 TCCCCTTACC 0.886793 -27 CTTTAAAAATTTCACTTAAAGAACAAAAGA 6 94 1 TTCACTTAAA 0.701256 -207 ATGATTTGACTTCCAATAACTCACTTAAAA 6 139 1 TTCCAATAAC 0.554118 -162 AACTACTAAATTTTATTAACCAAACAGCTT 6 276 0 TTTTATTAAC 0.720892 -25 TCCAGTGATATCCTTTTAAACTTTTTTAAA 7 51 0 TCCTTTTAAA 0.774268 -139 TCTTTTGTTTTTCTCTTAACCGCATCCCTT 7 122 0 TTCTCTTAAC 0.961437 -68 TTAAAATAATTGTTCTTAACT 9 75 1 TGTTCTTAAC 0.804929 -11 ********** Masking position 8 Map Score: 3.59408 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 109 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 ********** No masking Map Score: 1.66429e-14 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: 1.66429e-14 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: 1.66429e-14 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