AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_mpneu_reg_100.orf -o087_mpneu_100.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 0.499253 -284 cttaattcgctcgagaagatttttaaggcaaagaaaga 1 63 1 taaattttag 0.96123 -238 tgaccttagatttaaataatatttataacctaaaagac 1 265 1 tatattttaa 0.658878 -36 aattgattaattatcaatgtctttacggaactgtgcgg 3 17 1 taagttttag 0.982137 -166 tattctcaatttacaaaaaattttttggtgaaaaagtc 3 85 0 taaaattttg 0.655646 -98 tttttgtaaattgagaataaatttatgaaacttttagt 3 104 1 taaaatttaa 0.8314 -79 ttttaatgtgggaaagattttttatacgcattatca 3 157 0 taaattttta 0.607471 -26 gaaacctaagtaacgaaagtagttactgctacggctaa 4 26 1 taagtgttag 0.969919 -275 agtgtggtggtgcataaagtatttagaaaaatggtggt 4 193 0 taagttttaa 0.968595 -108 gtcgttaccgttattactgtcgttagtgtggtggtgca 4 217 0 tacgtgttag 0.846849 -84 aaactggtcgtcgataatgtcgttaccgttattactgt 4 235 0 taagtgttag 0.969845 -66 cagtttggcttcgtaaatgtttttaacaaccagttttt 4 267 1 taagttttaa 0.693751 -34 atcaataaaacttataaaatctttaacgt 6 34 1 caaattttag 0.851027 -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 atatttttaaaaacgcaaaagaaaataa 1 5 0 acgaaaagaa 0.978208 -296 aagatttttaaggcaaagaaagaacaattgtttt 1 78 1 acaagaaaaa 0.962416 -223 ggtagtcaccagacgaaaaaataacgcgaaaaac 1 107 0 acgaaaaaaa 0.985231 -194 ttcaatgataatgcgtataaaaaatctttcccac 3 152 1 acgataaaaa 0.974245 -31 tacggttattagccgtagcagtaactactttcgt 4 38 0 acgagcagaa 0.97612 -263 tacggctaataaccgtagaaataacgaacccctg 4 55 1 acgagaaaaa 0.99496 -246 aacccctgaaaatcgaagaaaaaaataaggtaga 4 81 1 acgagaaaaa 0.99496 -220 * ** ***** ** Masking position 7 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 atttaacattcgtctggtagtcaccagacga 1 125 0 cgtctggtgt 0.918597 -176 tagggtggcgaaggcggtatttttaaagagt 1 159 0 aaggcggttt 0.843003 -142 acctaaggataaggtggtaatttcgatccaa 4 133 0 aaggtggtat 0.920017 -168 ttatacactaaggctggtattaacaaaaaaa 4 163 1 aggctggttt 0.963117 -138 agtatttagaaaaatggtggtttttttgtta 4 183 0 aaaatggtgt 0.922488 -118 tactgtcgttagtgtggtggtgcataaagta 4 210 0 agtgtggtgt 0.970011 -91 ttacgaagccaaactggtcgtcgataatgtc 4 252 0 aaactggtgt 0.984153 -49 atgactaaaaactggttgttaaaaacatt 4 282 0 aaactggtgt 0.984153 -19 ******** ** Masking position 8 Map Score: 4.60813 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 89 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 tttttaaaaacgcaaaagaaaataa 1 5 0 ccaaaagaaa 0.737319 -296 gaattaaggccttaaacgacaacgtttgtta 1 40 0 ctaaacgaca 0.969509 -261 atatttataacctaaaagactgaaatcc 1 283 1 ctaaaagact 0.925903 -18 ccgcacagttccgtaaagacattgataatta 3 24 0 cgtaaagaca 0.980608 -159 ttagccgtagcagtaactactttcgttactt 4 33 0 cgtaactact 0.848097 -268 tgcaccaccacactaacgacagtaataacgg 4 217 1 cctaacgaca 0.982163 -84 acagtaataacggtaacgacattatcgacga 4 235 1 cgtaacgaca 0.987686 -66 acgttaaagattttataagttt 6 41 0 cttaaagatt 0.722236 -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 cccacaggagaattggtgaactcatgcgag 1 229 1 aattggtgaa 0.972422 -72 tttccgaattgattaattatcaatgt 3 7 1 aattgattaa 0.93394 -176 acaaaaaattttttggtgaaaaagtcgaga 3 81 0 ttttggtgaa 0.921756 -102 attgagaataaatttatgaaacttttagtt 3 113 1 aatttatgaa 0.888461 -70 aatggtggtttttttgttaataccagcctt 4 172 0 tttttgttaa 0.608758 -129 gcaattggcaaaatgatgaaaaaggaggac 5 60 1 aaatgatgaa 0.858397 -27 ttataagttttattgattaaccccagcggg 6 21 0 tattgattaa 0.915665 -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 6 cgtttgttaaatatttttaaaaacgcaaaa 1 19 0 atatttttaa 0.941399 -282 tcgctcgagaagatttttaaggcaaagaaa 1 69 1 agatttttaa 0.95567 -232 ttaaagagttatatttaacattcgtctggt 1 138 0 atatttaaca 0.71414 -163 ggcgaaggcggtatttttaaagagttatat 1 154 0 gtatttttaa 0.751572 -147 gatttaaataatatttataacctaaaagac 1 273 1 atatttataa 0.864813 -28 tttagttgctagattattcaatgataatgc 3 136 1 agattattca 0.839783 -47 aatgtgggaaagattttttatacgcattat 3 159 0 agatttttta 0.930741 -24 ccttatccttaggttatacactaaggctgg 4 150 1 aggttataca 0.444915 -151 ggcttcgtaaatgtttttaacaaccagttt 4 273 1 atgtttttaa 0.860445 -28 cttaaatttaatatttattaggtacaaaaa 5 23 0 atatttatta 0.799547 -64 acgttaaagattttataagttttattg 6 36 0 agattttata 0.842589 -17 ********** Masking position 10 Map Score: 6.02508 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 80 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 caattgtttttcgcgttattttttcgtctggtg 1 102 1 tgcgttattt 0.772182 -199 accgccttcgccaccctaagcttgggtgcgtgg 1 172 1 caccctactt 0.94766 -129 cgagggtccttgaccttagatttaaataatatt 1 255 1 taccttattt 0.928104 -46 acttaggtttctgacttacacttgaa 4 4 0 cgacttactt 0.933442 -297 acaagttggtctaccttatttttttcttcgatt 4 91 0 caccttattt 0.982593 -210 atcgaaattaccaccttatccttaggttataca 4 137 1 caccttactt 0.985542 -164 ttgttaataccagccttagtgtataacctaagg 4 156 0 cgccttagta 0.878266 -145 caattgctaacaggcttaaatttaatatttatt 5 34 0 cggcttattt 0.945092 -53 * ****** *** Masking position 8 Map Score: 1.5683 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 123 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 acgattccacaatctagcaagatgccacgc 1 199 0 aatctagcaa 0.989026 -102 tgcggctacgaaaatagcaaatttcaaaac 3 50 1 aaaatagcaa 0.949579 -133 atcattgaataatctagcaactaaaagttt 3 131 0 aatctagcaa 0.989026 -52 ********** Masking position 6 Map Score: 0.605286 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 12 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 9 gcgtttttaaaaatatttaacaaacgttgt 1 23 1 aaatatttaa 0.923392 -278 ttttaaagagttatatttaacattcgtctg 1 140 0 ttatatttaa 0.894098 -161 gtccttgaccttagatttaaataatattta 1 260 1 ttagatttaa 0.790358 -41 tagatttaaataatatttataacctaaaag 1 271 1 taatatttat 0.923392 -30 ggcttaaatttaatatttattaggtacaaa 5 25 0 taatatttat 0.923392 -62 aaaacttataaaatctttaacgt 6 40 1 aaatctttaa 0.81684 -13 ********** Masking position 6 Map Score: 1.53256 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 11 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 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 Motif number 12 ********** 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