AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_Glycerol_Uptake_mgen_reg_300.orf -o030_mgen_300.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/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 RMG02184 264 Mycoplasma #2 RMG01136 197 Mycoplasma #3 RMG05235 158 Mycoplasma Motif number 1 ATTTCGATCTTTTATTTTGATTTTTTTAATAAACGCTT 1 8 0 TTTTTTTTAA 0.989681 -257 ACTGCTTTTTTTTTTTTTTTTTTTACGAAAAAGTGGCTAAA 1 70 0 TTTTTTTAAA 0.992786 -195 TAAACCTTCTTTTGGTTAGTTCTTACTAACAGTTTTAAATG 1 151 1 TTTTTTTAAA 0.992786 -114 AGCAATAATATTTATTTAAACGTTAATGATATAAAAC 2 7 0 TTTTCTTAAA 0.865971 -191 TGCTAACAAGTTTAAAGTAATCTTAGCAATAATATTTATTT 2 31 0 TTTATTTAAA 0.951908 -167 GTTAGCAAACTTTAATCATTTTTTAGCTAAATTAAACAACC 2 65 1 TTTTTTTAAA 0.992686 -133 ATTAGTTAGTTTTTATTTTGTATTTTCAAAATTCTACTCAA 2 143 1 TTTTTTTTAA 0.989041 -55 TTTTTTATCTTTTGATTTCTTTTTACTAAAAATAATTAGCT 3 26 0 TTTTTTTAAA 0.992786 -133 TAAAAAAATGTTTGATACTACTTTTTATAGAGATACCAAAA 3 60 1 TTTTCTTTAA 0.976358 -99 TCTTCTAGTATTTAGTTAGTTATTTTGCAAAAAAGGATTAG 3 121 0 TTTTTTTTAA 0.968664 -38 *** * * *** * * Masking position 13 Map Score: 22.713 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 78 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 AAGCGTTTATTAAAAAAATCAAAAT 1 2 1 ACTTTATAAA 0.896821 -263 ATAAATTTCGATCTTTTATTTTGATTTTTTTAAT 1 19 0 ACTTTATTTA 0.865531 -246 TATCAATAATTATTTTTAGTTTTAGCCACTTTTT 1 50 1 TTTTTATTTA 0.646511 -215 AGTTTTAGCCACTTTTTCGTAAAAAAAAAAAAAA 1 67 1 ATTTTCTAAA 0.720111 -198 AAAAAAAAGCAGTTTTTGCTATTTTAGACTAAAA 1 98 1 ATTTTGTATT 0.931307 -167 AAGAAGGTTTAAATTTTGGTATATAACCACTTTT 1 128 0 AATTTGTATT 0.771248 -137 AATTTAAACCTTCTTTTGGTTAGTTCTTACTAAC 1 147 1 TCTTTGTTAT 0.717021 -118 TAACATTTAAAACTGTTAGTAAGAACTAACCAAA 1 161 0 ACGTTATAAA 0.774405 -104 AAAAACTTCAAATAGTTGTTTATTCTGTATCTAA 1 220 1 ATGTTGTTAT 0.896916 -45 TTGAAAGATTAAAGGTTAATTAGATACAGAATAA 1 239 0 AAGTTATTAA 0.595456 -26 TCTTAGCAATAATATTTATTTAAACGTTAATGAT 2 18 0 ATTTTATTAA 0.937441 -180 AAAAATGATTAAAGTTTGCTAACAAGTTTAAAGT 2 54 0 AATTTGTAAA 0.845652 -144 TTACTAATTAACTGGTTGTTTAATTTAGCTAAAA 2 85 0 ATGTTGTTAT 0.896917 -113 TAATTCTGGAACTGTTTACTAATTAACTGGTTGT 2 100 0 ATTTTATAAT 0.925672 -98 AAAACTAACTAATATTTGATTTTAATTCTGGAAC 2 122 0 ATTTTGTTTA 0.942244 -76 AATATTAGTTAGTTTTTATTTTGTATTTTCAAAA 2 140 1 ATTTTATTTT 0.902168 -58 TTTAGCTAATTATTTTTAGTAAAAAGAAATCAAA 3 23 1 TTTTTATAAA 0.71179 -136 ACATTTTTTTATCTTTTGATTTCTTTTTACTAAA 3 37 0 ACTTTGTTTT 0.904415 -122 AAGATAAAAAAATGTTTGATACTACTTTTTATAG 3 56 1 ATTTTGTACA 0.776529 -103 GTTGTGATTTACTTTTTGGTATCTCTATAAAAAG 3 80 0 ATTTTGTATT 0.931307 -79 TTAATCTTCTAGTATTTAGTTAGTTATTTTGCAA 3 132 0 ATTTTATTAT 0.931749 -27 * * **** *** * Masking position 7 Map Score: 24.0699 Number of sites scoring better than the average of aligned sites = 813 Number in coding regions = 703 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 GCTAAAACTAAAAATAATTATTGATAAATT 1 46 0 AAAATAATTA 0.956245 -219 TTTTTACGAAAAAGTGGCTAAAACTAAAAA 1 62 0 AAAGTGGCTA 0.949294 -203 CTTTTAGTCTAAAATAGCAAAAACTGCTTT 1 103 0 AAAATAGCAA 0.783242 -162 TTTTAGACTAAAAGTGGTTATATACCAAAA 1 119 1 AAAGTGGTTA 0.94528 -146 AGATTACTTTAAACTTGTTAGCAAACTTTA 2 49 1 AAACTTGTTA 0.767744 -149 ATTTAGCTAAAAAATGATTAAAGTTTGCTA 2 67 0 AAAATGATTA 0.965713 -131 TACAAAATAAAAACTAACTAATATTTGATT 2 135 0 AAACTAACTA 0.930634 -63 CTTTTTACTAAAAATAATTAGCTAAAATAC 3 19 0 AAAATAATTA 0.956245 -140 TATTTTGCAAAAAAGGATTAGTTTTATAGT 3 112 0 AAAAGGATTA 0.854528 -47 CCTTTTTTGCAAAATAACTAACTAAATACT 3 126 1 AAAATAACTA 0.959518 -33 ********** Masking position 3 Map Score: 12.5342 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 170 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TTATATACCAAAATTTAAACCTTCTTTTGGTT 1 136 1 AATTTAAACT 0.747666 -129 AACTTGTGTAACATTTAAAACTGTTAGTAAGA 1 171 0 ACTTTAAACT 0.90598 -94 TCAAAGTGTGAATTTAAAAACTTCAAATAGTT 1 205 1 AATTAAAACT 0.925371 -60 TATCTAATTAACCTTTAATCTTTCAATA 1 247 1 ACTTTAATTT 0.635333 -18 TATTTATTTAAACGTTAATGATATAAAAC 2 8 0 AAGTTAATAT 0.709249 -190 TTGCTAAGATTACTTTAAACTTGTTAGCAAAC 2 43 1 TATTTAAATT 0.53342 -155 CTTGTTAGCAAACTTTAATCATTTTTTAGCTA 2 62 1 AATTTAATAT 0.868806 -136 ACTAATATTTGATTTTAATTCTGGAACTGTTT 2 117 0 GATTTAATCT 0.880973 -81 TTGAAAATACAAAATAAAAACTAACTAATATT 2 140 0 AAATAAAACT 0.67537 -58 AATTGAGTAGAATTTTGAAAATACAAAATAAA 2 154 0 AATTTGAAAT 0.778601 -44 AGTAAATCACAACTATAAAACTAATCCTTTTT 3 101 1 AATATAAACT 0.874906 -58 ** ****** ** Masking position 8 Map Score: 3.8116 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 462 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 ACTAAAAATAATTATTGATAAATTTCGATC 1 40 0 ATTATTGATA 0.886175 -225 AAAAAAAGCAGTTTTTGCTATTTTAGACTA 1 99 1 GTTTTTGCTA 0.952304 -166 AGAAGGTTTAAATTTTGGTATATAACCACT 1 131 0 AATTTTGGTA 0.918176 -134 TTAAATAAATATTATTGCTAAGATTACTTT 2 29 1 ATTATTGCTA 0.959604 -169 AAAATGATTAAAGTTTGCTAACAAGTTTAA 2 57 0 AAGTTTGCTA 0.961682 -141 CTGGTTGTTTAATTTAGCTAAAAAATGATT 2 78 0 AATTTAGCTA 0.94194 -120 AATTGAGTAGAATTTTGAAAATACAAAATA 2 156 0 AATTTTGAAA 0.841716 -42 ATATGACGGTATTTTAGCTAATTATTTTTA 3 11 1 ATTTTAGCTA 0.959602 -148 AGATAAAAAAATGTTTGATACTACTTTTTA 3 57 1 ATGTTTGATA 0.923328 -102 AAACTAATCCTTTTTTGCAAAATAACTAAC 3 118 1 TTTTTTGCAA 0.789239 -41 ********** Masking position 5 Map Score: 11.226 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 220 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ********** No masking Map Score: -6.01529e-13 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: -6.01529e-13 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: -6.01529e-13 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