AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_mgen_reg_300.orf -o00640_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 MG357 300 acetate kinase (ackA) #2 MG460 172 L-lactate dehydrogenase (ldh) Motif number 1 TTGAATAGATAAAGAATCCAGAAGACAATAGCA 1 16 1 AAAAACAGAA 0.798235 -285 TTGCTAATACAAAAAATACAGTTGCTACTGTTT 1 65 1 AAAAAAAGTT 0.885496 -236 TAACAGATGTTAATAATGCAAAAACAGTAGCAA 1 86 0 TAAAAGAAAA 0.682544 -215 AAAAAGTAAAAAAGAAAACCAATAAAAGCTGAA 1 136 1 AAAAAACAAT 0.950105 -165 ATAAAAGCTGAAATAACAGCGATAATATAGCAT 1 157 1 AAAAAACGAT 0.944457 -144 AATGAAAATTAAAAAATGCTATATTATCGCTGT 1 172 0 AAAAAGTATA 0.896568 -129 ATTAAATCTTAAACAATGAAAATTAAAAAATGC 1 186 0 AAAAAGAAAT 0.974197 -115 AACTAAAAAGAAATATTATTAAATCTTAAACAA 1 203 0 AAAATATAAA 0.741005 -98 ATTTATTAAAAAATAATACTAAATTAATATAGT 1 256 0 AAAAAATAAA 0.949906 -45 ATTTTTTAATAAATAAGGTAAATATTCTTCGGT 1 275 1 AAAAAGAAAT 0.974196 -26 TGTTACAAATAATTATAATATCGCTCATC 2 7 1 AAAAATTAAT 0.808284 -166 ACTGTTATTTAAAGATGAGCGATATTATAATTA 2 20 0 AAAATACGAT 0.719543 -153 GCTCATCTTTAAATAACAGTGTTGTTTTGTAAT 2 33 1 AAAAAATGTT 0.885496 -140 TTTGTAATCCAAAAAAAGTAAATTCAGGCAACA 2 58 1 AAAAAGAAAT 0.974196 -115 TGCTTTGTCTAAATAAGGATATTTGAAGTCAAA 2 95 0 AAAAAGTATT 0.924389 -78 ATCCTTATTTAGACAAAGCAAAATTTATTAAAG 2 108 1 AGAAAGAAAA 0.761144 -65 AAGTGAACCAAAATAAAATTGAAGTATATCTCT 2 138 1 AAAAAATGAA 0.944236 -35 *** ** * **** Masking position 5 Map Score: 20.1261 Number of sites scoring better than the average of aligned sites = 778 Number in coding regions = 680 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 TTTTTTTGAATAGATAAAGAAT 1 3 1 TTTTTGAATA 0.954722 -298 CAACTGTATTTTTTGTATTAGCAACATTAA 1 59 0 TTTTGTATTA 0.973049 -242 TTGCTACTGTTTTTGCATTATTAACATCTG 1 86 1 TTTTGCATTA 0.929279 -215 ATTGGTTTTCTTTTTTACTTTTTATCTTCA 1 129 0 TTTTTTACTT 0.924263 -172 TAATATAGCATTTTTTAATTTTCATTGTTT 1 179 1 TTTTTTAATT 0.918728 -122 ACTATATTAATTTAGTATTATTTTTTAATA 1 256 1 TTTAGTATTA 0.850639 -45 TTTAGTATTATTTTTTAATAAATAAGGTAA 1 266 1 TTTTTTAATA 0.955578 -35 AATTTACTTTTTTTGGATTACAAAACAACA 2 52 0 TTTTGGATTA 0.97252 -121 AGGCAACAGTTTTTTGACTTCAAATATCCT 2 83 1 TTTTTGACTT 0.922849 -90 ********** Masking position 7 Map Score: 12.0075 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 195 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 ACAATAGCATTAACAACTATTAATGTTGCT 1 40 1 TAACAACTAT 0.898612 -261 TTTTTTGTATTAGCAACATTAATAGTTGTT 1 51 0 TAGCAACATT 0.976761 -250 GCAAAAACAGTAGCAACTGTATTTTTTGTA 1 72 0 TAGCAACTGT 0.986437 -229 TTTGCATTATTAACATCTGTTATCCCTATA 1 97 1 TAACATCTGT 0.879668 -204 TTGGATTACAAAACAACACTGTTATTTAAA 2 40 0 AAACAACACT 0.929257 -133 AAGTAAATTCAGGCAACAGTTTTTTGACTT 2 73 1 AGGCAACAGT 0.957226 -100 TATTTAGACAAAGCAAAATTTATTAAAGTG 2 113 1 AAGCAAAATT 0.807206 -60 ********** Masking position 5 Map Score: 3.59344 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 214 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 AGAAGACAATAGCATTAACAACTATTAATG 1 35 1 AGCATTAACA 0.912194 -266 TTTTTGTATTAGCAACATTAATAGTTGTTA 1 50 0 AGCAACATTA 0.948908 -251 CTTCACTTATAGGGATAACAGATGTTAATA 1 104 0 AGGGATAACA 0.949508 -197 CTGAAATAACAGCGATAATATAGCATTTTT 1 164 1 AGCGATAATA 0.987634 -137 TTAACTAAAAAGAAATATTATTAAATCTTA 1 208 0 AGAAATATTA 0.90683 -93 TTTAAAGATGAGCGATATTATAATTATTTG 2 16 0 AGCGATATTA 0.987634 -157 ********** Masking position 7 Map Score: 4.10407 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 83 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TTTTTTTGAATAGATAAAGAATCCAGAAG 1 10 1 ATAGATAAAG 0.878004 -291 TGTTATCCCTATAAGTGAAGATAAAAAGTA 1 114 1 ATAAGTGAAG 0.954192 -187 AAAAAGAAATATTATTAAATCTTAAACAAT 1 202 0 ATTATTAAAT 0.722573 -99 ATAGTGTGGAATAATTAAATGTTTTAACTA 1 231 0 ATAATTAAAT 0.948841 -70 TTATTTTTTAATAAATAAGGTAAATATTCT 1 273 1 ATAAATAAGG 0.849667 -28 AACAACACTGTTATTTAAAGATGAGCGATA 2 29 0 TTATTTAAAG 0.659074 -144 GTAATCCAAAAAAAGTAAATTCAGGCAACA 2 61 1 AAAAGTAAAT 0.776317 -112 CTAAATAAGGATATTTGAAGTCAAAAAACT 2 90 0 ATATTTGAAG 0.907252 -83 GAACCAAAATAAAATTGAAGTATATCTCTA 2 142 1 AAAATTGAAG 0.895888 -31 ATATCTCTAGATAAATAAAT 2 163 1 ATAAATAAAT 0.919815 -10 ********** Masking position 6 Map Score: 6.67389 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 239 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 ********** No masking Map Score: 3.08538e-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 7 ********** No masking Map Score: 3.08538e-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 8 ********** No masking Map Score: 3.08538e-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