AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i036_Acetate_Metabolism_mpneu_reg_300.orf -o036_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 RMP00406 300 Mycoplasma_pneumoniae #2 RMP00408 55 Mycoplasma_pneumoniae #3 RMP00409 157 Mycoplasma_pneumoniae #4 RMP00412 30 Mycoplasma_pneumoniae #5 RMP00414 37 Mycoplasma_pneumoniae Motif number 1 caattggtgataagcggattaaaacaggaa 1 13 1 taagcggatt 0.942271 -288 tagttagataaaagcaggttagttaaagca 1 57 1 aaagcaggtt 0.991753 -244 gccaagagattaagctagttgcaccagtgg 1 170 1 taagctagtt 0.926916 -131 agtgggcactaaagcagtttttcttactta 1 195 1 aaagcagttt 0.983578 -106 tggcactttaaaagctagtttttacctaaa 1 237 0 aaagctagtt 0.925384 -64 taacgcggtttttgctctcta 1 290 0 aacgcggttt 0.689834 -11 aaacaaatcgttagcacttttagcgtttga 2 14 0 ttagcacttt 0.867492 -42 acataaaaaaagagcagtttaactgccctc 3 37 0 agagcagttt 0.964684 -121 tagacgtctttaagcactttttaaaccatt 3 93 1 taagcacttt 0.963978 -65 taaaactaagtaagcaggttttt 5 25 1 taagcaggtt 0.993395 -13 ********** Masking position 9 Map Score: 15.0058 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 192 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 acgttttttttttttttttgaaagaaattg 1 89 0 tttttttttg 0.868023 -212 aatctcttggcttaattttgtacattttaa 1 151 0 cttaattttg 0.967363 -150 cttatcaatacttatttttaggtaaaaact 1 221 1 cttattttta 0.977291 -80 actttaaaagctagtttttacctaaaaata 1 233 0 ctagttttta 0.824811 -68 taaatttttgctttattttggcactttaaa 1 255 0 ctttattttg 0.961609 -46 tgtttatgtgctaaatattataaacaaatc 2 35 0 ctaaatatta 0.741675 -21 taactgccctctttttattgatctactgca 3 18 0 ctttttattg 0.869715 -140 ttcaattagtcttatttttaaaatttaaaa 3 125 1 cttattttta 0.977291 -33 tttaagtttttatttttaaattttaaaa 3 140 0 tttattttta 0.904766 -18 tctaattagtttatattttactact 4 6 0 ttatatttta 0.704904 -25 tagttttactctttactttaat 5 3 0 ctttacttta 0.839536 -35 aacctgcttacttagttttactctttactt 5 15 0 cttagtttta 0.929782 -23 ********** Masking position 8 Map Score: 14.5438 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 314 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 agcaggttagttaaagcaatcaatttcttt 1 69 1 ttaaagcaat 0.976428 -232 tttgtacattttaaaccacgatggcatgac 1 135 0 ttaaaccacg 0.951511 -166 atgtacaaaattaagccaagagattaagct 1 156 1 ttaagccaag 0.878444 -145 aagtgccaaaataaagcaaaaatttaacct 1 259 1 ataaagcaaa 0.911956 -42 gctaaatattataaacaaatcgttagcact 2 26 0 ataaacaaat 0.823559 -30 aaagacgtctataaaccattattacaggtc 3 74 0 ataaaccatt 0.938659 -84 tatagacgtctttaagcactttttaaacca 3 91 1 tttaagcact 0.767476 -67 taagcactttttaaaccattttttcaatta 3 103 1 ttaaaccatt 0.957271 -55 gtagtaaaatataaactaattagaggatt 4 12 1 ataaactaat 0.891471 -19 attaaagtaaagagtaaaact 5 2 1 ttaaagtaaa 0.749116 -36 ********** Masking position 4 Map Score: 7.40394 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 373 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 aaacaggaatagatttacttaaatagttag 1 34 1 agatttactt 0.784234 -267 aacgttttttttttttttttgaaagaaatt 1 90 0 tttttttttt 0.669163 -211 taaagcagtttttcttacttatcaatactt 1 204 1 tttcttactt 0.934532 -97 ttacttatcaatacttatttttaggtaaaa 1 218 1 atacttattt 0.907366 -83 gttaaatttttgctttattttggcacttta 1 257 0 tgctttattt 0.857954 -44 tctttttttatgtcttatttgacctgtaat 3 54 1 tgtcttattt 0.970109 -104 tttttcaattagtcttatttttaaaattta 3 122 1 agtcttattt 0.952898 -36 tttaagtttttatttttaaatttta 3 143 0 gtttttattt 0.824298 -15 aaaaacctgcttacttagttttactcttta 5 18 0 ttacttagtt 0.828623 -20 ********** Masking position 5 Map Score: 4.13065 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 154 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 ctgcttttatctaactatttaagtaaatct 1 44 0 ctaactattt 0.970151 -257 ttagttaaagcaatcaatttctttcaaaaa 1 75 1 caatcaattt 0.922701 -226 cttacaatttcaaacgtttttttttttttt 1 102 0 caaacgtttt 0.914267 -199 gcatgacaaacttacaatttcaaacgtttt 1 112 0 cttacaattt 0.945755 -189 gctaaaagtgctaacgatttgtttataata 2 20 1 ctaacgattt 0.988151 -36 ********** Masking position 8 Map Score: 2.79935 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 38 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 tagttgcaccagtgggcactaaagcagttt 1 185 1 agtgggcact 0.844125 -116 tttaacctttagagagcaaaaaccgcgtta 1 281 1 agagagcaaa 0.955201 -20 atcaataaaaagagggcagttaaactgctc 3 26 1 agagggcagt 0.994806 -132 agacataaaaaaagagcagtttaactgccc 3 39 0 aaagagcagt 0.97358 -119 ********** Masking position 8 Map Score: 0.85056 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 16 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 7 ********** No masking Map Score: 1.60826e-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: 1.60826e-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: 1.60826e-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