AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_mpneu_reg_300.orf -o087_mpneu_300.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMP00078 300 Mycoplasma_pneumoniae #2 RMP00102 17 Mycoplasma_pneumoniae #3 RMP00103 182 Mycoplasma_pneumoniae #4 RMP00192 300 Mycoplasma_pneumoniae #5 RMP00213 86 Mycoplasma_pneumoniae #6 RMP00214 52 Mycoplasma_pneumoniae Motif number 1 tcttttgcgtttttaaaaatatttaacaaacgttgtcg 1 17 1 taaattttaa 0.499306 -284 cttaattcgctcgagaagatttttaaggcaaagaaaga 1 63 1 taaattttag 0.961332 -238 tgaccttagatttaaataatatttataacctaaaagac 1 265 1 tatattttaa 0.662746 -36 aattgattaattatcaatgtctttacggaactgtgcgg 3 17 1 taagttttag 0.982605 -166 tattctcaatttacaaaaaattttttggtgaaaaagtc 3 85 0 taaaattttg 0.663952 -98 tttttgtaaattgagaataaatttatgaaacttttagt 3 104 1 taaaatttaa 0.836351 -79 ttttaatgtgggaaagattttttatacgcattatca 3 157 0 taaattttta 0.607267 -26 gaaacctaagtaacgaaagtagttactgctacggctaa 4 26 1 taagtgttag 0.971003 -275 agtgtggtggtgcataaagtatttagaaaaatggtggt 4 193 0 taagttttaa 0.969493 -108 gtcgttaccgttattactgtcgttagtgtggtggtgca 4 217 0 tacgtgttag 0.851682 -84 aaactggtcgtcgataatgtcgttaccgttattactgt 4 235 0 taagtgttag 0.970926 -66 cagtttggcttcgtaaatgtttttaacaaccagttttt 4 267 1 taagttttaa 0.689986 -34 atcaataaaacttataaaatctttaacgt 6 34 1 caaattttag 0.853828 -19 * ** ** **** * Masking position 6 Map Score: 12.9596 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 108 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 ttattttcttttgcgtttttaaaaatat 1 5 1 ttcttttcgt 0.977838 -296 aaaacaattgttctttctttgccttaaaaatctt 1 78 0 tttttcttgt 0.961789 -223 gtttttcgcgttattttttcgtctggtgactacc 1 107 1 tttttttcgt 0.984978 -194 gtgggaaagattttttatacgcattatcattgaa 3 152 0 tttttatcgt 0.97381 -31 acgaaagtagttactgctacggctaataaccgta 4 38 1 ttctgctcgt 0.975716 -263 caggggttcgttatttctacggttattagccgta 4 55 0 tttttctcgt 0.994873 -246 tctaccttatttttttcttcgattttcaggggtt 4 81 0 tttttctcgt 0.994873 -220 ** ***** ** * Masking position 8 Map Score: 8.50233 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 5 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 3 gtctggtagtcaccagacgaaaaaataacg 1 115 0 caccagacga 0.974182 -186 gtctggtgactaccagacgaatgttaaata 1 127 1 taccagacga 0.97468 -174 ataccgccttcgccaccctaagcttgggtg 1 170 1 cgccacccta 0.95735 -131 tgtggaatcgtcccacaggagaattggtga 1 218 1 tcccacagga 0.906204 -83 aaaaaatctttcccacattaaaa 3 170 1 tcccacatta 0.921441 -13 ggatcgaaattaccaccttatccttaggtt 4 135 1 taccacctta 0.944706 -166 tttttgttaataccagccttagtgtataac 4 162 0 taccagcctt 0.873396 -139 ctttatgcaccaccacactaacgacagtaa 4 212 1 caccacacta 0.984284 -89 ********** Masking position 5 Map Score: 4.64812 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 80 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 tttttaaaaacgcaaaagaaaataa 1 5 0 ccaaaagaaa 0.728188 -296 gaattaaggccttaaacgacaacgtttgtta 1 40 0 ctaaacgaca 0.968099 -261 atatttataacctaaaagactgaaatcc 1 283 1 ctaaaagact 0.922639 -18 ccgcacagttccgtaaagacattgataatta 3 24 0 cgtaaagaca 0.979701 -159 ttagccgtagcagtaactactttcgttactt 4 33 0 cgtaactact 0.841992 -268 tgcaccaccacactaacgacagtaataacgg 4 217 1 cctaacgaca 0.981328 -84 acagtaataacggtaacgacattatcgacga 4 235 1 cgtaacgaca 0.987106 -66 acgttaaagattttataagttt 6 41 0 cttaaagatt 0.712784 -12 * ********* Masking position 6 Map Score: 4.69919 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 77 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ttctcaatttacaaaaaattttttggtgaaa 3 90 0 acaaaaattt 0.829881 -93 taatctagcaactaaaagtttcataaattta 3 121 0 acaaaagttt 0.962203 -62 ccaaaaatagtccacaagttggtctacctta 4 106 0 tcacaagttg 0.871732 -195 taacaaaaaaaccaccatttttctaaatact 4 183 1 acaccatttt 0.957808 -118 gacattatcgacgaccagtttggcttcgtaa 4 252 1 acaccagttt 0.991629 -49 aatgtttttaacaaccagtttttagtcat 4 282 1 acaccagttt 0.991629 -19 ** ******** Masking position 7 Map Score: 3.18031 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 73 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 cccacaggagaattggtgaactcatgcgag 1 229 1 aattggtgaa 0.976307 -72 tttccgaattgattaattatcaatgt 3 7 1 aattgattaa 0.942927 -176 acaaaaaattttttggtgaaaaagtcgaga 3 81 0 ttttggtgaa 0.93228 -102 attgagaataaatttatgaaacttttagtt 3 113 1 aatttatgaa 0.902992 -70 aatggtggtttttttgttaataccagcctt 4 172 0 tttttgttaa 0.645176 -129 gcaattggcaaaatgatgaaaaaggaggac 5 60 1 aaatgatgaa 0.8763 -27 ttataagttttattgattaaccccagcggg 6 21 0 tattgattaa 0.926944 -32 ********** Masking position 9 Map Score: 2.33661 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 133 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 cgtttgttaaatatttttaaaaacgcaaaa 1 19 0 atatttttaa 0.955142 -282 tcgctcgagaagatttttaaggcaaagaaa 1 69 1 agatttttaa 0.958452 -232 ttaaagagttatatttaacattcgtctggt 1 138 0 atatttaaca 0.643302 -163 ggcgaaggcggtatttttaaagagttatat 1 154 0 gtatttttaa 0.816196 -147 gatttaaataatatttataacctaaaagac 1 273 1 atatttataa 0.905992 -28 tttagttgctagattattcaatgataatgc 3 136 1 agattattca 0.685937 -47 aatgtgggaaagattttttatacgcattat 3 159 0 agatttttta 0.934981 -24 ggcttcgtaaatgtttttaacaaccagttt 4 273 1 atgtttttaa 0.816197 -28 cttaaatttaatatttattaggtacaaaaa 5 23 0 atatttatta 0.857347 -64 acgttaaagattttataagttttattg 6 36 0 agattttata 0.799895 -17 ********** Masking position 5 Map Score: 6.57517 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 35 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 ttgtttttcgcgttattttttcgtctggtg 1 105 1 cgttattttt 0.838188 -196 gggtccttgaccttagatttaaataatatt 1 258 1 ccttagattt 0.963585 -43 tactttcgttacttaggtttctgacttaca 4 17 0 acttaggttt 0.917801 -284 agttggtctaccttatttttttcttcgatt 4 91 0 ccttattttt 0.957612 -210 accaccttatccttaggttatacactaagg 4 146 1 ccttaggtta 0.9748 -155 ttaataccagccttagtgtataacctaagg 4 156 0 ccttagtgta 0.929091 -145 ********** Masking position 5 Map Score: 1.48664 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 84 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 ********** No masking Map Score: 6.56131e-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 10 ********** No masking Map Score: 6.56131e-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: 6.56131e-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