AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_mpneu_reg_100.orf -o255_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 Purged sequences: RMP00035 22 Mycoplasma_pneumoniae Input sequences: #1 RMP00031 31 Mycoplasma_pneumoniae #2 RMP00036 300 Mycoplasma_pneumoniae #3 RMP00134 45 Mycoplasma_pneumoniae #4 RMP00137 300 Mycoplasma_pneumoniae #5 RMP00406 300 Mycoplasma_pneumoniae #6 RMP00408 55 Mycoplasma_pneumoniae Motif number 1 gcggctaacaaaataaaattaggataa 1 8 1 acaaaataaa 0.973227 -24 atccgtgatttcgaaattaaaccattagca 2 69 1 tcgaaattaa 0.962061 -232 gacattcacgacaaaattaagtattcctgt 2 147 0 acaaaattaa 0.983139 -154 attagtaagctcacaattaatattttgacg 3 17 0 tcacaattaa 0.922449 -29 tttttgatgaacgaaattaatattctggcg 4 281 0 acgaaattaa 0.970607 -20 tcaatttctttcaaaaaaaaaaaaaaaacg 5 88 1 tcaaaaaaaa 0.833412 -213 tttaaaatgtacaaaattaagccaagagat 5 150 1 acaaaattaa 0.983139 -151 ttttaaagtgccaaaataaagcaaaaattt 5 254 1 ccaaaataaa 0.942447 -47 ********** Masking position 5 Map Score: 9.62272 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 68 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 ggctaacaaaataaaattaggataaccta 1 13 1 ataaaatagg 0.712942 -19 tgcgaattacattgaaccagtacttggcgac 2 29 1 attgaacagt 0.903931 -272 tgatttcgaaattaaaccattagcaatttaa 2 74 1 attaaacatt 0.839662 -227 acctcacataactaaaacaggaatacttaat 2 131 1 actaaacagg 0.950723 -170 cgtgaatgtcgttaaggcggtttcgatagtg 2 167 1 gttaagcggt 0.751268 -134 tctcaaccatattaaaataattaaatattcg 2 258 0 attaaataat 0.723525 -43 tattaatataattaaatcggtttcgatcaaa 4 246 1 attaaacggt 0.949742 -55 tgataagcggattaaaacaggaatagattta 5 20 1 attaaacagg 0.98389 -281 aaatagttagataaaagcaggttagttaaag 5 54 1 ataaaacagg 0.925793 -247 aagcaggttagttaaagcaatcaatttcttt 5 68 1 gttaaacaat 0.806963 -233 aatgtacaaaattaagccaagagattaagct 5 155 1 attaagcaag 0.871905 -146 aagccaagagattaagctagttgcaccagtg 5 168 1 attaagtagt 0.857144 -133 accagtgggcactaaagcagtttttcttact 5 192 1 actaaacagt 0.949449 -109 ****** **** Masking position 5 Map Score: 11.2082 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 348 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 tagggggtgtggttaaaccacctcacataactaa 2 112 1 ggtaccactc 0.989386 -189 aagtagtgacggttaatccatttcacgccaacac 2 208 1 ggttccattc 0.971596 -93 ttgcaaataagattctttcatctcaaccatatta 2 275 0 gatttcactc 0.961243 -26 agattgatcagtatattctaattcaatccgcaaa 4 11 0 gtttctattc 0.741494 -290 tgcaaacctagaaattaccacctctacttcccag 4 44 1 gaaaccactc 0.960867 -257 gactaaacgtgagtcctccaactcccaaactctg 4 75 0 gattccactc 0.995077 -226 cccctacatcgagttgactatctcgtggactaaa 4 102 0 gatactactc 0.804621 -199 ctcgtgtggggactattcccactccagctaccaa 4 162 0 gattcccctc 0.983328 -139 ** * **** *** Masking position 13 Map Score: 6.60461 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 31 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 4 cacaacgttaccgaatatttaattattttaa 2 247 1 cgaatattta 0.956176 -54 tagtttcgtcaaaatattaattgtgagctt 3 10 1 caaatattaa 0.980033 -36 catgtccaagcgaagtattaatataattaaa 4 231 1 caagtattaa 0.956747 -70 aaaaattcgccagaatattaatttcgttcat 4 274 1 cgaatattaa 0.976024 -27 ctgcttttatctaactatttaagtaaatcta 5 43 0 caactattta 0.922199 -258 tgtttatgtgctaaatattataaacaaatcg 6 34 0 caaatattat 0.923732 -22 * ********* Masking position 6 Map Score: 2.76326 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 14 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 5 ctaagcttcgttaaattgctaatggtttaatt 2 83 0 taaattgcaa 0.95167 -218 atattctaattcaatccgcaaa 4 1 0 taatccgcaa 0.93784 -300 aatatactgatcaatctgcaaacctagaaatt 4 28 1 taatctgcaa 0.976339 -273 aaactagcttttaaagtgccaaaataaagcaa 5 246 1 taaagtgcaa 0.990365 -55 aatttaacctttagagagcaaaaaccgcgtta 5 279 1 tagagagcaa 0.885633 -22 actcaaacgctaaaagtgctaacgatttgttt 6 12 1 taaagtgcaa 0.990365 -44 atgtttatgtgctaaatattataaa 6 41 0 ttatgtgcaa 0.94247 -15 * ******* ** Masking position 11 Map Score: 4.07032 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 36 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 6 tcaatgtaattcgcaactacgattttgaat 2 14 0 tcgcaactac 0.95215 -287 tggtttaatttcgaaatcacggattttagt 2 63 0 tcgaaatcac 0.977782 -238 gttcccactatcgaaaccgccttaacgaca 2 173 0 tcgaaaccgc 0.990649 -128 tctgcaaacctagaaattaccacctctact 4 42 1 tagaaattac 0.789772 -259 gaatttttgatcgaaaccgatttaattata 4 252 0 tcgaaaccga 0.951551 -49 ********** Masking position 5 Map Score: 0.671648 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 21 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ttacattgaaccagtacttggcgacggaact 2 35 1 ccgtacttgg 0.974376 -266 aaccacaccccctaagcttcgttaaattgct 2 95 0 ccaagcttcg 0.947677 -206 cctctacttcccagagtttgggagttggagg 4 64 1 ccgagtttgg 0.938498 -237 ccttcatttacctgaacttggtagctggagt 4 145 1 ccgaacttgg 0.993065 -156 atagtccccacacgagattggttgactcgat 4 180 1 cagagattgg 0.941503 -121 ** ******** Masking position 8 Map Score: 0.623641 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 23 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 agtacttggcgacggaactaaaatccgtga 2 47 1 gacggaacta 0.981793 -254 ggtttcgatagtgggaacggtctaagtagt 2 185 1 gtgggaacgg 0.958055 -116 ttaatattttgacgaaacta 3 1 0 gacgaaacta 0.911766 -45 ccaatctcgtgtggggactattcccactcc 4 171 0 gtggggacta 0.985079 -130 agttgcaccagtgggcactaaagcagtttt 5 186 1 gtgggcacta 0.985061 -115 ********** Masking position 7 Map Score: 0.605681 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 10 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 taaattgctaatggtttaatttcgaaatca 2 74 0 atggtttaat 0.793186 -227 gttatgtgaggtggtttaaccacaccccct 2 113 0 gtggtttaac 0.974582 -188 ttggcgtgaaatggattaaccgtcactact 2 209 0 atggattaac 0.931583 -92 tttgcggattgaattagaatata 4 4 1 gcggattgaa 0.925766 -297 tgactatctcgtggactaaacgtgagtcct 4 92 0 gtggactaaa 0.948804 -209 ttggtgataagcggattaaaacaggaatag 5 16 1 gcggattaaa 0.975921 -285 tcatgccatcgtggtttaaaatgtacaaaa 5 136 1 gtggtttaaa 0.978838 -165 ********** Masking position 9 Map Score: 5.6728 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 85 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ********** No masking Map Score: 1.48036e-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 11 ********** No masking Map Score: 1.48036e-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 12 ********** No masking Map Score: 1.48036e-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