AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_mgen_reg_300.orf -o087_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 Purged sequences: RMG02201 20 Mycoplasma Input sequences: #1 RMG00079 158 Mycoplasma #2 RMG00127 300 Mycoplasma #3 RMG01190 300 Mycoplasma #4 RMG05389 59 Mycoplasma #5 RMG03249 115 Mycoplasma Motif number 1 TTTTTTGCAAAATAACTAACTAAATACTAGAAG 1 19 0 ATAAAACTAA 0.971802 -140 GTAAATCACAACTATAAAACTAATCCTTTTTTG 1 45 0 ATATAACTAA 0.964362 -114 TTTTACTAAAAATAATTAGCTAAAATACCGTCA 1 133 1 ATAAAGCTAA 0.823818 -26 AGCTAATTGTTTTTTAGAACAAACTGAATCAAA 2 49 1 TTTTAACAAA 0.824399 -252 TGTTAACAGCATTTAACAACAAAATTGAATAAA 2 103 1 ATTAAACAAA 0.971801 -198 ATTGAATAAAAATAAAAAACAGACCCTGATGGT 2 126 1 ATAAAACAGA 0.9336 -175 TCCGCCATTAAATATCCAACAGACCATCAGGGT 2 148 0 ATATAACAGA 0.916942 -153 TTTATAATAAATTTAACAACAAACTGGGAGCGT 2 255 0 ATTAAACAAA 0.971801 -46 ATTTATTATAAATATGCAACTAATTAGCGCTTT 2 276 1 ATATAACTAA 0.964362 -25 ACCTTAGGTTTTTTAACAACAAATGGGATAGCA 3 45 0 TTTAAACAAA 0.856757 -256 TATCATACTAATTATTAAACAAACCAATGCCAA 3 244 0 ATATAACAAA 0.977641 -57 AAACCATTTTCTTTTCCAACTAATTGATCATTA 4 13 0 CTTTAACTAA 0.707246 -47 TTTCGTTGCCATTATTGCACTAAGCTTAATATT 5 29 1 ATATCACTAA 0.774346 -87 CTAATAAGATAGTAAATAAGAAATTATTAATTA 5 63 1 ATAAAAGAAA 0.815203 -53 ATAAGAAATTATTAATTACCAAAATTATTAAAA 5 78 1 ATAAACCAAA 0.88426 -38 AGTTAAGAACAATTATTTTAATA 5 103 0 ATTAAACAAT 0.74676 -13 * *** ****** Masking position 3 Map Score: 18.0478 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 227 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 GCAAAAAAGGATTAGTTTTATAGTTGTGATT 1 44 1 ATTAGTTTAT 0.981507 -115 CTCTATAAAAAGTAGTATCAAACATTTTTTT 1 88 1 AGTAGTATAA 0.894623 -71 AGCTTTTAAAATTAGTCTAATGTAAATTCTG 2 16 0 ATTAGTCTAT 0.665733 -285 TAAAGCGCTAATTAGTTGCATATTTATAATA 2 279 0 ATTAGTTGAT 0.96885 -22 TTGTTTAATAATTAGTATGATAGTTGGTAGT 3 255 1 ATTAGTATAT 0.979502 -46 GATAGTTGGTAGTAGTATTATCATTGGCTAT 3 273 1 AGTAGTATAT 0.964028 -28 TTAATGATCAATTAGTTGGAAAAGAAAATGG 4 12 1 ATTAGTTGAA 0.90771 -48 TTACTATCTTATTAGTAATATTAAGCTTAGT 5 47 0 ATTAGTAAAT 0.919343 -69 GTTAAGAACAATTATTTTAATAATTTTGGTA 5 94 0 ATTATTTTAT 0.810695 -22 ******** ** Masking position 6 Map Score: 9.4224 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 51 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 TATCTTTTGATTTCTTTTTACTAAAAATAA 1 118 1 TTTCTTTTTA 0.881197 -41 TTTGATTCAGTTTGTTCTAAAAAACAATTA 2 52 0 TTTGTTCTAA 0.899654 -249 GAAATTGTCTTTCATTGTTAACAGCATTTA 2 88 1 TTCATTGTTA 0.874003 -213 TTTATTCAATTTTGTTGTTAAATGCTGTTA 2 106 0 TTTGTTGTTA 0.989662 -195 GGGTCTGTTTTTTATTTTTATTCAATTTTG 2 122 0 TTTATTTTTA 0.898216 -179 ACGCTCCCAGTTTGTTGTTAAATTTATTAT 2 255 1 TTTGTTGTTA 0.989662 -46 TGCTATCCCATTTGTTGTTAAAAAACCTAA 3 45 1 TTTGTTGTTA 0.989662 -256 TATTAAAATAATTGTTCTTAACT 5 103 1 ATTGTTCTTA 0.899672 -13 ********** Masking position 10 Map Score: 9.27204 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 114 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 TCTAGTATTTAGTTAGTTATTTTGCAAAAA 1 21 1 AGTTAGTTAT 0.860813 -138 TCTTTGATTCAGTTTGTTCTAAAAAACAAT 2 54 0 AGTTTGTTCT 0.956502 -247 TTTTTATTCAATTTTGTTGTTAAATGCTGT 2 108 0 ATTTTGTTGT 0.804863 -193 GTACGCTCCCAGTTTGTTGTTAAATTTATT 2 253 1 AGTTTGTTGT 0.976784 -48 CCAGCAATTAAGTTAGCAGTTAACATCACC 3 75 0 AGTTAGCAGT 0.948978 -226 GGTGTTTTTGTGTTTGCACTTTTAAAAACT 3 163 1 TGTTTGCACT 0.778898 -138 TGCCAACTCCAGTTTGTAATGTAGCTCCTT 3 209 0 AGTTTGTAAT 0.945985 -92 TACAAACTGGAGTTGGCATTGGTTTGGCAT 3 221 1 AGTTGGCATT 0.846463 -80 TTAGTATGATAGTTGGTAGTAGTATTATCA 3 266 1 AGTTGGTAGT 0.972128 -35 ********** Masking position 4 Map Score: 7.20286 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 115 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 ATTAGCTACAGCTTTTAAAATTAGTCTAAT 2 26 0 GCTTTTAAAA 0.938844 -275 TAGCACCTTCACTAATAAAACTCAATCCCA 3 20 0 ACTAATAAAA 0.974727 -281 TTGTGTTTGCACTTTTAAAAACTACTTTAC 3 170 1 ACTTTTAAAA 0.95797 -131 GTTTTTGAAAACTTATAAAATCTTTCAT 4 42 1 ACTTATAAAA 0.964668 -18 CGAAAATAGAGCTAATAAAAGAA 5 4 0 GCTAATAAAA 0.962955 -112 GCTTAATATTACTAATAAGATAGTAAATAA 5 52 1 ACTAATAAGA 0.921753 -64 AATTACCAAAATTATTAAAATAATTGTTCT 5 91 1 ATTATTAAAA 0.794268 -25 ********** Masking position 7 Map Score: 7.48898 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 136 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 CGGTGGGATTCGAACCCACGCACCGTAGAA 2 183 1 CGAACCCACG 0.952869 -118 TAATAAAACTCAATCCCATCAGATAAC 3 8 0 CAATCCCATC 0.972113 -293 AGTGAAGGTGCTATCCCATTTGTTGTTAAA 3 37 1 CTATCCCATT 0.877285 -264 GTAGCTCCTTCAATCCCTTGTAAAGTAGTT 3 189 0 CAATCCCTTG 0.96716 -112 AAACCAATGCCAAACCAATGCCAACTCCAG 3 227 0 CAAACCAATG 0.976395 -74 AATTATTAAACAAACCAATGCCAAACCAAT 3 238 0 CAAACCAATG 0.976395 -63 ********** Masking position 3 Map Score: 3.42686 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 38 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ATATGACGGTATTTTAGCTAATT 1 146 0 TGACGGTATT 0.856554 -13 TTAGATCGTTCTACGGTGCGTGGGTTCGAA 2 191 0 CTACGGTGCG 0.928689 -110 GGACACCCTGCTAAGGTGTTAGATCGTTCT 2 209 0 CTAAGGTGTT 0.957062 -92 GTTTTATTAGTGAAGGTGCTATCCCATTTG 3 29 1 TGAAGGTGCT 0.983591 -272 GTTAAAAAACCTAAGGTGATGTTAACTGCT 3 61 1 CTAAGGTGAT 0.898182 -240 GTGCTCCTCATGGCGGTGTTTTTGTGTTTG 3 149 1 TGGCGGTGTT 0.934059 -152 TACAAGGGATTGAAGGAGCTACATTACAAA 3 197 1 TGAAGGAGCT 0.925621 -104 ********** Masking position 5 Map Score: 2.1731 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 27 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 TGCTCCACAAATTGCTCCAGCAATTAAGTT 3 91 0 ATTGCTCCAG 0.977403 -210 TGCTCCTGTTAATGCTCCACAAATTGCTCC 3 103 0 AATGCTCCAC 0.987068 -198 TGATAAGGCAAATGCTCCTGTTAATGCTCC 3 115 0 AATGCTCCTG 0.987031 -186 CTTATCAATTCGTGCTCCTCATGGCGGTGT 3 138 1 CGTGCTCCTC 0.974112 -163 ********** Masking position 6 Map Score: 1.04863 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 8 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 CTATAAAACTAATCCTTTTTTGCAAAATAA 1 37 0 AATCCTTTTT 0.755867 -122 TTATCTTTTGATTTCTTTTTACTAAAAATA 1 117 1 ATTTCTTTTT 0.925889 -42 TATTTTAGCTAATTATTTTTAGTAAAAAGA 1 130 0 AATTATTTTT 0.788865 -29 AGCTGTAGCTAATTGTTTTTTAGAACAAAC 2 43 1 AATTGTTTTT 0.970982 -258 AAGAATTTGAAATTGTCTTTCATTGTTAAC 2 80 1 AATTGTCTTT 0.86304 -221 TTTTATTCAATTTTGTTGTTAAATGCTGTT 2 107 0 TTTTGTTGTT 0.765709 -194 TACGCTCCCAGTTTGTTGTTAAATTTATTA 2 254 1 GTTTGTTGTT 0.82888 -47 GTGCTATCCCATTTGTTGTTAAAAAACCTA 3 44 1 ATTTGTTGTT 0.958723 -257 TGGAAAAGAAAATGGTTTTTGAAAACTTAT 4 28 1 AATGGTTTTT 0.874659 -32 GTAATTAATAATTTCTTATTTACTATCTTA 5 67 0 ATTTCTTATT 0.721736 -49 TTATTAAAATAATTGTTCTTAACT 5 102 1 AATTGTTCTT 0.911474 -14 ********** Masking position 6 Map Score: 7.44194 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 345 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 ********** No masking Map Score: 1.58751e-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 11 ********** No masking Map Score: 1.58751e-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 12 ********** No masking Map Score: 1.58751e-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