AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i301_mixed16_mgen_reg_300.orf -o301_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 RMG00022 300 Mycoplasma #2 RMG01110 46 Mycoplasma #3 RMG00025 65 Mycoplasma #4 RMG02159 188 Mycoplasma #5 RMG01114 41 Mycoplasma #6 RMG00035 29 Mycoplasma #7 RMG02168 26 Mycoplasma #8 RMG00037 202 Mycoplasma #9 RMG04456 38 Mycoplasma #10 RMG03425 36 Mycoplasma #11 RMG04443 58 Mycoplasma Motif number 1 TATTTTGGTTAAATTAAAATTGTTATAATAATTAGTTA 1 229 0 AAATAAATAA 0.955604 -72 GCTGTTTTGATTATAAAAACTGTTAAAATTCGAGGGGT 1 266 0 TTATAAATAA 0.843538 -35 TGAAGTAATTAATCTCTTTAAAATCTTTCAAGA 2 24 0 TAATAATTAA 0.983404 -23 ATAAATTTAATAGTGTTGAAAGACaAACATT 3 4 1 AATTAATTAA 0.909334 -62 CTCAAAAAACTAATACATCAAACTTCAACCGTTTACTT 4 11 1 TAATCATTAA 0.932648 -178 AATCTATTTGAAATAATTCTTCATAAAACCTTTGTAGT 4 63 0 AAATATTTAA 0.955605 -126 AATGGGAATGTTTTCAAATCTTCTTAAATAATCTATTT 4 92 0 TTTTAAATAA 0.48419 -97 TTCTGCTAAATCAATGGTTTTGTAATCATCAAAAA 4 164 0 AAATAATTAA 0.985179 -25 AGCAAGAATTATAATTAACACTCTAAGGATGCAAGT 5 9 1 TTATATTTAA 0.861479 -33 AAATCAATAAAATTCTAATACTACTTTT 6 12 0 AAATAATTAA 0.985179 -18 AAATTAATCTATTTTCAAAATGAGTTTT 8 1 1 AAATAATTAA 0.985179 -202 CATTAATTTTTAATTAATAAATGTTGAAAAAACTCATT 8 29 0 TAATAATTAA 0.983425 -174 TATTAATTAAAAATTAATGCTTTTTAAAGTTGAATCTT 8 48 1 AAATAATTAA 0.985179 -155 AAGTATTGAAAAATGAATTAAGATTCAACTTTAAAAAG 8 67 0 AAATAATTAA 0.985179 -136 GATAATATACTTATTTATCTAATATTCCAACA 9 5 1 ATATCTTTAA 0.619276 -34 AGCTAATAATTAAAAGTCTAATTTTTATTGT 10 16 0 TAATATTTAA 0.950085 -21 TATATATTAATAATTAAACATTTTAAAAGTCTTATAAA 11 28 0 TAATAAATAA 0.950241 -31 **** *** * ** Masking position 14 Map Score: 29.9291 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 156 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 AATTAGCTGTTTTGATTATAAAAACTGTTAAA 1 277 0 TTTGATTTAA 0.821954 -24 GACaAACATTATTAATTTTTGATCAGCTAAAT 3 32 1 ATTAATTTTA 0.927664 -34 ACTTCAACCGTTTACTTTTTTATGAACAAGCA 4 32 1 TTTACTTTTA 0.964749 -157 ATCTATTTGAAATAATTCTTCATAAAACCTTT 4 68 0 AATAATTTTA 0.886991 -121 GAGTGTTAATTATAATTCTTGCT 5 2 0 TATAATTTTC 0.752574 -40 TAGATATGCTTGTTAACTTTAAATTG 7 5 1 TATGCTTTTA 0.818373 -22 TTTAAAAAGCATTAATTTTTAATTAATAAATG 8 44 0 ATTAATTTTA 0.927662 -159 TTCATTTTTCAATACTTTTTTAGGCTTCCTAT 8 88 1 AATACTTTTA 0.854576 -115 AGCGTATTAATTTAATTAAAGAATAGGAAGCC 8 110 0 TTTAATTAAA 0.595378 -93 TTTCTTAACTTTTACTTTTAGAAAAGCGTATT 8 134 0 TTTACTTTAA 0.927757 -69 AAAACGTTTTTATAATTTTAGAGATAGTT 8 184 1 TATAATTTAA 0.913061 -19 GATAATATACTTATTTATCTAATATTC 9 6 1 TATACTTTTA 0.943768 -33 AAAGTCTAATTTTTATTGTTAATT 10 3 0 TTTTATTTTA 0.782841 -34 AAATTAGACTTTTAATTATTAGCT 10 23 1 TTTAATTTTG 0.832488 -14 AATTCGATTATTTAATTTTATAAGACTTTTAA 11 12 1 TTTAATTTAA 0.94148 -47 TTTTAAAATGTTTAATTATTAATATATAGCT 11 38 1 TTTAATTTTA 0.973421 -21 ******* ** * Masking position 6 Map Score: 20.3836 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 139 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 TTATAATCAAAACAGCTAATTTT 1 288 1 AACAGATTTT 0.719307 -13 AAAGATTTTAAAGAGATTAATTACTTCA 2 29 1 AAGAGAATTA 0.861465 -18 AATTATTTCAAATAGATTATTTAAGAAGATTTG 4 83 1 AATAGATTTA 0.917532 -106 AACAGTTTTAAAAAGCGCAATTTGATTCTTATC 4 133 0 AAAAGAATTT 0.95239 -56 TGTAATCATCAAAAACAGTTTTAAAAAGCGCAA 4 146 0 AAAAATTTTA 0.803658 -43 GAAAAGTAGTATTAGAATTTTATT 6 2 1 AAAAGTATTA 0.952692 -28 TCATTTTGAAAATAGATTAATTT 8 1 0 AATAGAATTT 0.876165 -202 TAAATGTTGAAAAAACTCATTTTGAAAATAGAT 8 17 0 AAAAAATTTT 0.753043 -186 AAAAGTATTGAAAAATGAATTAAGATTCAACTT 8 74 0 AAAAAATTAA 0.685478 -129 TTACTTTTAGAAAAGCGTATTAATTTAATTAAA 8 122 0 AAAAGATTAA 0.872939 -81 ACGCTTTTCTAAAAGTAAAAGTTAAGAAAAGTA 8 137 1 AAAAGAAGTT 0.693836 -66 AAAAGTTAAGAAAAGTACTTTTATTCAAACAAA 8 153 1 AAAAGTTTTA 0.940093 -50 TTATTCAAACAAAAACGTTTTTATAATTTTAGA 8 173 1 AAAAATTTTA 0.803658 -30 ATATTAGATAAATAAGTATATTATC 9 3 0 AATAATATTA 0.691779 -36 GCTAATAATTAAAAGTCTAATTTTTATTGTTAA 10 13 0 AAAAGAATTT 0.95239 -24 TATAAAATTAAATAATCGAATTA 11 1 0 AATAAAATTA 0.814105 -58 TAAACATTTTAAAAGTCTTATAAAATTAAATAA 11 19 0 AAAAGTATAA 0.813752 -40 AAGACTTTTAAAATGTTTAATTATTAATATATA 11 33 1 AAATGAATTA 0.74897 -26 ***** ***** Masking position 2 Map Score: 16.5428 Number of sites scoring better than the average of aligned sites = 741 Number in coding regions = 675 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 ATTATAACAATTTTAATTTAACCAAAATACC 1 238 1 TTTAATTTAA 0.933295 -63 AAATTAGCTGTTTTGATTATAAAAACTGTTA 1 279 0 TTTGATTATA 0.698215 -22 CTTTCAACACTATTAAATTTAT 3 2 0 TTTAAATTTA 0.858971 -64 AGACaAACATTATTAATTTTTGATCAGCTAA 3 31 1 TTTAATTTTT 0.93333 -35 AAGTTTGATGTATTAGTTTTTTGAG 4 5 0 TTTAGTTTTT 0.655131 -184 TTTCAAATCTTCTTAAATAATCTATTTGAAA 4 88 0 TTTAAATAAT 0.451062 -101 GCAATTTGATTCTTATCTTTAATGGGAATGT 4 119 0 TTTATCTTTA 0.556796 -70 ATCCTTAGAGTGTTAATTATAATTCTTGCT 5 10 0 TTTAATTATA 0.94804 -32 TAGATATGCTTGTTAACTTTAAATTG 7 11 1 TTTAACTTTA 0.932081 -16 TTTCAACATTTATTAATTAAAAATTAATGCT 8 38 1 TTTAATTAAA 0.894956 -165 TAGAAAAGCGTATTAATTTAATTAAAGAATA 8 117 0 TTTAATTTAA 0.933247 -86 AAAGTACTTTTCTTAACTTTTACTTTTAGAA 8 143 0 TTTAACTTTT 0.865648 -60 AAAAACGTTTTTATAATTTTAGAGATAGTT 8 183 1 TATAATTTTA 0.827938 -20 AAAATTAGACTTTTAATTATTAGCT 10 22 1 TTTAATTATT 0.895474 -15 TAATTCGATTATTTAATTTTATAAGACTTTT 11 11 1 ATTAATTTTA 0.718427 -48 AGCTATATATTAATAATTAAACATTTTAAAA 11 38 0 TATAATTAAA 0.579836 -21 * ********* Masking position 4 Map Score: 15.8271 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 306 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 TTTAATGGTGGAGATGAAGGGTCTCAAACCC 1 45 1 GAGATAAGGG 0.963973 -256 TTGCACTCAGGAGGTTGAGGGTTTGAGACCC 1 63 0 GAGGTGAGGG 0.989651 -238 ATTATTGGTGGAAGTAAATGGACTTGAACCA 1 126 1 GAAGTAATGG 0.976581 -175 TGATAAGGGTGAGGTCGATGGTTCAAGTCCA 1 144 0 GAGGTGATGG 0.983822 -157 AAAACTGTTAAAATTCGAGGGGTATTTTGGT 1 258 0 AAATTGAGGG 0.836794 -43 TGTTCATAAAAAAGTAAACGGTTGAAGTTTG 4 29 0 AAAGTAACGG 0.892072 -160 TTCTGCTAAATCAATGGTTTTGTAATC 4 172 0 TAAATAATGG 0.729742 -17 ***** ***** Masking position 8 Map Score: 1.79718 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 25 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TGGAATTCTTTAATGGTGGAGATGAAGGGTC 1 37 1 TAATGGTGAG 0.928469 -264 TGATTTGCACTCAGGAGGTTGAGGGTTTGAG 1 67 0 TCAGGAGGTG 0.851915 -234 CTTCCACCAATAATGGGGATGTAGCTCAACT 1 109 0 TAATGGGGTG 0.98939 -192 ACACCCCTGATAAGGGTGAGGTCGATGGTTC 1 151 0 TAAGGGTGGG 0.961191 -150 CTCACCCTTATCAGGGGTGTGCTCTAACCAA 1 162 1 TCAGGGGTTG 0.941205 -139 AGCATAATCCTAAGGGTATTTAACTAATTAT 1 209 1 TAAGGGTATT 0.713778 -92 ATAAATTTAATAGTGTTGAAAGACaAAC 3 8 1 TAATAGTGTG 0.87654 -58 TTCTTATCTTTAATGGGAATGTTTTCAAATC 4 110 0 TAATGGGATG 0.962175 -79 TCTGCTAAATCAATGGTTTTGTAATCATCAA 4 167 0 CAATGGTTTG 0.821922 -22 ******** ** Masking position 3 Map Score: 2.71086 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 139 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ********** No masking Map Score: -2.84684e-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 8 ********** No masking Map Score: -2.84684e-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 9 ********** No masking Map Score: -2.84684e-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