AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i099_mgen_mpneu_300.orf -o099_mgen_mpneu_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -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 = 0.36 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMG05422 23 Mycoplasma RMG03267 55 Mycoplasma Input sequences: #1 RMG04313 147 Mycoplasma #2 RMG04312 64 Mycoplasma #3 RMG03266 52 Mycoplasma #4 RMG03264 97 Mycoplasma #5 RMG03260 188 Mycoplasma #6 RMP00228 300 Mycoplasma_pneumoniae #7 RMP00229 85 Mycoplasma_pneumoniae #8 RMP00231 114 Mycoplasma_pneumoniae #9 RMP00232 241 Mycoplasma_pneumoniae Motif number 1 GAAATGCATTTTTATTAATTGCAAAT 1 6 0 TTTTTAATTG 0.873011 -142 TGACACTCAGGTTATTATTTAGTCTAGTTTT 1 60 0 GTTTTATTTA 0.909755 -88 TTTAAAGAAATTTCTAAACTTTAGCACTTTT 1 127 0 TTTTAAACTT 0.854975 -21 CAAATTTTAATTGCTAATCTTTAAGGTAC 4 9 0 TTGTAATCTT 0.602106 -89 ATATCTCTTTTTGATAATCTAGAACAGTGGG 4 60 1 TTGTAATCTA 0.651885 -38 GTTAAATGGCTTTGTTAATTTGTTTAGATGT 5 13 1 TTTTTAATTT 0.916502 -176 AATAAATATAGTTTTTATTTTTATTAATAAA 5 75 0 GTTTTATTTT 0.890416 -114 AATGAGCCGTTTTCTAATTTTGTTATAATTC 5 151 1 TTTTAATTTT 0.8138 -38 ATTCAACGTGTTTATTAATTA 5 178 1 TTTTTAATTA 0.931591 -11 cgatttcaccgttattaactgttgctgatga 6 59 0 gttttaactg 0.872849 -242 ttaatcctaagtttttagcttatgcacttag 6 231 1 gttttagctt 0.791602 -70 aatttaggtgtttctaatctaagtgcataag 6 249 0 ttttaatcta 0.868498 -52 aacacctaaatttgttaattatgcttgccct 6 268 1 tttttaatta 0.931591 -33 gctttaaagctttttaaatta 7 1 0 ttttaaatta 0.857241 -85 ttgaactaaagtttttaacttgccaattttt 7 43 0 gttttaactt 0.91639 -43 acaactgctttttgttattttttaaaagttt 8 11 0 tttttatttt 0.908355 -104 ttttttaaaagtttttatttatccgttttga 8 41 0 gttttattta 0.909755 -74 attaattcactttttcatctattaaattgct 8 93 0 ttttcatcta 0.670217 -22 gaaaatcgttgtttttaactacttaaagcac 9 170 1 gttttaacta 0.931498 -72 gcaagttgcatttcttagttgtgctttaagt 9 190 0 tttttagttg 0.704368 -52 gaaatgcaacttgcttaattaaaagttggtt 9 207 1 ttgttaatta 0.794697 -35 *** ******* Masking position 5 Map Score: 23.3993 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 550 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 ATGCATTTCATTTAAATTAATTGGCTTGTGAA 1 28 1 TTTAATAATT 0.869035 -120 TTTAGCACTTTTTAAACAGATTAAATCTTTTC 1 107 0 TTTAAAGATT 0.941434 -41 TTTAAAGAAATTTCTAAACTTT 1 136 0 TTTAAAAATT 0.976251 -12 TAAATGTGTATTTAATGAAATATTGACAATTT 2 27 0 TTTAAAAATA 0.935031 -38 TACACATTTATTTAATGAGATAAATT 2 49 1 TTTAAAGATA 0.849127 -16 AATCTATACATCTAAACAAATTAACAAAGCCA 5 19 0 TCTAAAAATT 0.866375 -170 TTTTTATTTTTATTAATAAATTCTCTCGATAT 5 63 0 TATTAAAATT 0.871095 -126 TACTTATTACTTATAATAAATATAGTTTTTAT 5 88 0 TTATAAAATA 0.587107 -101 CACGTTGAATTATAACAAAATTAGAAAACGGC 5 156 0 TATAAAAATT 0.917032 -33 taatttaaaaagctttaaagcacta 7 4 1 tttaaagctt 0.862747 -82 acttgccaatttttagaaaattagtgctttaa 7 25 0 ttttaaaatt 0.96177 -61 aaacttttaaaaaataacaaaaagca 8 5 1 ttttaaaata 0.897925 -110 aaataaaaacttttaaaaaattggcgtcaatt 8 52 1 ttttaaaatt 0.96177 -63 cagcctctcgtaaaaagaaattagcaaaggaa 9 114 1 taaaaaaatt 0.640841 -128 aaatcgttgtttttaactacttaaagcacaac 9 172 1 ttttatactt 0.613618 -70 ttcggtactttttaaccaacttttaattaagc 9 219 0 tttaaaactt 0.941434 -23 ***** ***** Masking position 5 Map Score: 17.4847 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 185 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 TTTCATTTAAATTAATTGGCTTGTGAAAAA 1 33 1 ATTAATTGGC 0.95037 -115 AACTAGCAATAAAAATTGTCAATATTTCAT 2 15 1 AAAAATTGTC 0.952387 -50 ATTTTTATTAATAAATTCTCTCGATATTTT 5 60 0 ATAAATTCTC 0.928655 -129 GTTAGAAGTAATAAATTCTCCTACTTACTT 5 115 0 ATAAATTCTC 0.928655 -74 attggttgcgttaaattgaccgttacgata 6 167 0 ttaaattgac 0.804549 -134 ctaattttctaaaaattggcaagttaaaaa 7 33 1 aaaaattggc 0.976407 -53 tttacattcaataaattgaactaaagtttt 7 59 0 ataaattgaa 0.718965 -27 aaaacttttaaaaaattggcgtcaattccc 8 57 1 aaaaattggc 0.976407 -58 aattaattcactttttcatct 8 104 0 attaattcac 0.804446 -11 tagcaaaggaaacaattggcaaagaataaa 9 135 1 aacaattggc 0.916392 -107 ********** Masking position 5 Map Score: 9.78523 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 42 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 CTCAGGTTATTATTTAGTCTAGTTTTTTCACAAGCCAAT 1 47 0 TTTTTTATTC 0.977799 -101 AGAGATATTTTCTTTAGCATGTACCTTTCAAATTTTAAT 4 29 0 TTTTCTGTTC 0.971407 -69 tcctggattgtttttgatatatagtttgctgat 6 5 0 ttttttattc 0.977799 -296 aaatcacaatcctttatcttaccgatttcaccgttatta 6 73 0 ctttctattc 0.953525 -228 atttcatcactttttaccttaagaattccacaaacattg 6 193 0 ttttctattc 0.979473 -108 tgaactaaagtttttaacttgccaatttttagaaaatta 7 34 0 ttttctgttt 0.769086 -52 tagttcaatttattgaatgtaaagattgcc 7 66 1 tttgttattc 0.949843 -20 cgagaggctgcttttcttttaatcattcaaccaatggcc 9 85 0 ctttttatta 0.649925 -157 ctttgccaattgtttcctttgctaatttctttttacgag 9 120 0 ttttttgttc 0.969096 -122 acaacgattttctggcgtttattctttgccaattgtttc 9 143 0 ttggttattc 0.797954 -99 * *** * ** ** * Masking position 10 Map Score: 4.07837 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 46 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TTTAGTCTAGTTTTTTCACAAGCCAATTAAT 1 43 0 TTTTTCACAA 0.723153 -105 AATTTCTAAACTTTAGCACTTTTTAAACAGA 1 119 0 CTTAGCACTT 0.932465 -29 CGATGTTTTTTGCATATATTTAGATAC 3 36 0 TTTTGCATAT 0.541736 -17 ttaggattaatttcatcactttttaccttaa 6 210 0 tttatcactt 0.929663 -91 aagtttttagcttatgcacttagattagaaa 6 239 1 ctttgcactt 0.920754 -62 ttaaaaagctttaaagcactaattttctaaa 7 15 1 ttaagcacta 0.925959 -71 gttaaaaactttagttcaatttattgaatgt 7 55 1 ttattcaatt 0.531324 -31 caattccctttttgagcaatttaatagatga 8 79 1 tttagcaatt 0.861477 -36 aattaattcactttttcatctat 8 102 0 ttattcactt 0.867688 -13 atctggttagttttagcactagt 9 3 0 tttagcacta 0.954977 -239 ttttaactacttaaagcacaactaagaaatg 9 182 1 ttaagcacaa 0.832814 -60 *** ******* Masking position 8 Map Score: 4.94366 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 193 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ATAAAAATGCATTTCATTTAAATTAATTGG 1 22 1 ATTTCATTTA 0.741626 -126 GTCAATTCGAATTCTCTTTAGAAAAGATTT 1 87 1 ATTCTCTTTA 0.947522 -61 AAAGTTTAGAAATTTCTTTAAA 1 136 1 AATTTCTTTA 0.614368 -12 ACAAAACCGCATTCTATTTTAATATTA 3 8 0 ATTCTATTTT 0.838846 -45 AAAAAGAGATATTTTCTTTAGCATGTACCT 4 42 0 ATTTTCTTTA 0.918846 -56 atccaggagaattccctgtttattcatcag 6 36 1 attccctgtt 0.876504 -265 attggcgtcaattccctttttgagcaattt 8 71 1 attccctttt 0.971455 -44 aattaattcactttttcatctatta 8 100 0 attcactttt 0.867047 -15 cgagaggctgcttttcttttaatcattcaa 9 94 0 cttttctttt 0.77563 -148 tcctttgctaatttctttttacgagaggct 9 115 0 atttcttttt 0.704416 -127 ********** Masking position 7 Map Score: 4.36501 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 153 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ********** No masking Map Score: -3.55739e-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: -3.55739e-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: -3.55739e-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