AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_mgen_mpneu_100.orf -o020_mgen_mpneu_100.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: RMG05728 17 Mycoplasma RMP00447 21 Mycoplasma_pneumoniae Input sequences: #1 RMG05729 249 Mycoplasma #2 RMG03546 27 Mycoplasma #3 RMG03545 82 Mycoplasma #4 RMG04575 66 Mycoplasma #5 RMP00444 166 Mycoplasma_pneumoniae #6 RMP00445 67 Mycoplasma_pneumoniae #7 RMP00446 20 Mycoplasma_pneumoniae #8 RMP00448 300 Mycoplasma_pneumoniae Motif number 1 AGCTAGGTAACTATATTTTAAAAAAGTG 1 7 0 CTAATTTTAA 0.915761 -243 TTACCTAGCTTTATTTTTTAGAGCTAGGTACC 1 29 1 TTATTTTTAA 0.982612 -221 AAATTTTGTCTTACTTTTTACAGCAGCTGTTG 1 131 0 TTATTTTTAA 0.982612 -119 TACTGGCTTTTTAGTTGTTAGACAAAAATTTT 1 156 0 TTATTGTTAA 0.96297 -94 CTGGCTTTTTTTATTTGTTATAGATCACTACT 1 194 1 TTATTGTTAA 0.96297 -56 TACTTAAAGTTTAAATTTAATAGTAGTGATCT 1 215 0 TTAATTTAAA 0.930907 -35 CTTAGTTTTAAATTAGCATAGAt 2 2 1 TTATTTTAAT 0.85812 -26 CAAAAGCTTAATTTTAAAAGtTCGAATCA 3 8 1 TTATTTTAAA 0.969904 -75 TTTTAATAACTTAAATTTTATATAAATATTAA 4 14 0 TTAATTTTAA 0.959386 -53 ACCTCACTAACTATTTTTAATAACTTAAATTT 4 28 0 CTATTTTAAA 0.936838 -39 cgtgaaaatattaatcttaagacattgattac 6 43 1 ttatcttaaa 0.824611 -25 aattatttgttagtttaatc 7 7 0 ttattgttat 0.829931 -14 ataattgcacctagtttttttaactaaaagtt 8 46 1 ctatttttta 0.719062 -255 taaaaactgttttaattttagatttaaagcaa 8 275 0 tttattttaa 0.699234 -26 *** ****** * Masking position 8 Map Score: 18.4989 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 160 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 TAGCTCTAAAAAATAAAGCTAGGTAACTATATTTT 1 20 0 AATAAATGTA 0.651211 -230 TCATTTCATAAATTAAAGTGATGGAAGACAACAAG 1 61 1 AATAAAGGGA 0.776689 -189 CTGCTGTAAAAAGTAAGACAAAATTTTTGTCTAAC 1 137 1 AATAAGAATT 0.814659 -113 TTTGTCTAACAACTAAAAAGCCAGTAACTAAACTG 1 162 1 AATAAAGAGT 0.961564 -88 AAAAGCCAGTAACTAAACTGGCTTTTTTTATTTGT 1 177 1 AATAAAGTTT 0.878039 -73 CTACTATTAAATTTAAACTTTAAGTACTATCAATA 1 221 1 ATTAAATAGT 0.898079 -29 TTTTTAAGCTATTTAAGGATAATTTGTGCAGTAGT 3 39 0 ATTAAGTTTT 0.618334 -44 CTTAATATTTATATAAAATTTAAGTTATTAAAAAT 4 13 1 ATTAAATAGT 0.904518 -54 taccgcacttaactaaacttagtttggcgtgaaaa 6 16 1 aataaatttt 0.859125 -52 aagccatttgaaataagtttggggtttgttagaat 8 13 1 aataagtggt 0.870159 -288 tagtttttttaactaaaagttgagaaggctaggga 8 57 1 aataaataga 0.84303 -244 atgctgccaaaaataaggcgaaatttctctaaatt 8 188 1 aataaggatt 0.89515 -113 ctggctttttatctaaaacgaaatttagagaaatt 8 209 0 attaaagatt 0.879531 -92 aaagtaatgcaaataaaaaaccagtcttacgactg 8 241 0 aataaaaagt 0.927184 -60 ttaattttagatttaaagcaaaagtaatgcaaata 8 261 0 attaaaaagt 0.856695 -40 ttaaatctaaaattaaaacagtttttatatc 8 280 1 aataaaattt 0.785637 -21 ** **** * *** Masking position 6 Map Score: 11.8629 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 316 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 ATTCGCACTTGCATTGGCAGCATTTCTTGTTGTCT 1 86 0 GCAGCGCATT 0.99603 -164 ACTTTTTACAGCAGCTGTTGCACTTAGCGCATTCG 1 116 0 GCAGTGCATT 0.977464 -134 ATCGTATTGATAGTACTTAAAGTTTAAA 1 232 0 GTAATGTATT 0.766079 -18 ATATCTTAGCTGCAGTAATTTTTTAAGCTA 3 63 0 TTAGCGTATT 0.966277 -20 ctaagtttagttaagtgcggtatttat 6 3 0 ttagcgtatt 0.966277 -65 tttcggttttgcaaccacagcatttcttgtcttcc 8 116 0 gcaacgcatt 0.986071 -185 cgccacagttgcatttactgcagttagctgtttcg 8 146 0 gcaacgcatt 0.986071 -155 ggcagcatttgcaaccgccacagttgcatttactg 8 161 0 gcagcacatt 0.960932 -140 tttcgccttatttttggcagcatttgcaaccgcca 8 176 0 tttgcgcatt 0.904283 -125 gactggttttttatttgcattacttttgctttaaa 8 250 1 ttagcttatt 0.737463 -51 *** ** *** ** Masking position 12 Map Score: 9.72538 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 80 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 CAGTTTAGTTACTGGCTTTTTAGTTGTTAG 1 167 0 ACTGGCTTTT 0.968865 -83 CAGTAACTAAACTGGCTTTTTTTATTTGTT 1 183 1 ACTGGCTTTT 0.968865 -67 CAAAAGCTTAATTTTAAAAGt 3 2 1 AAAAGCTTAA 0.626924 -81 ATTATCCTTAAATAGCTTAAAAAATTACTG 3 51 1 AATAGCTTAA 0.858763 -32 GAGGTTCAAAAAGCGCTTTTCT 4 55 1 AAGCGCTTTT 0.917474 -12 gaaacgcttttaacagttttt 5 2 1 aaacgctttt 0.831491 -165 cagaaactccaagcgcttgatcgagctatt 5 51 1 aagcgcttga 0.865149 -116 aaagtcattaaatcgcttaatagctcgatc 5 69 0 aatcgcttaa 0.947372 -98 atcgtaatcaatgtcttaagattaatatt 6 49 0 aatgtcttaa 0.656145 -19 acttatttcaaatggcttga 8 1 0 aatggcttga 0.956581 -300 cagtcttacgactggctttttatctaaaac 8 225 0 actggctttt 0.968865 -76 cagtcgtaagactggttttttatttgcatt 8 241 1 actggttttt 0.696799 -60 ********** Masking position 1 Map Score: 12.1475 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 169 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 ATATAGTTACCTAGCTTTATTTTTTAGAGC 1 23 1 CTAGCTTTAT 0.863102 -227 AAAATTTTGTCTTACTTTTTACAGCAGCTG 1 134 0 CTTACTTTTT 0.858726 -116 AGTTTAGTTACTGGCTTTTTAGTTGTTAGA 1 166 0 CTGGCTTTTT 0.985931 -84 AGTAACTAAACTGGCTTTTTTTATTTGTTA 1 184 1 CTGGCTTTTT 0.985931 -66 TTGAACCTCACTAACTATTTTTAATAACTT 4 34 0 CTAACTATTT 0.815341 -33 gaaacgcttttaacagtttttaagataat 5 10 1 ttaacagttt 0.462603 -157 gagtttctgtttcactgtttattatcttaa 5 30 0 ttcactgttt 0.833363 -137 actcaaacaattcactgtttaaaaaaattg 5 133 0 ttcactgttt 0.833363 -34 ataattgcacctagtttttttaactaaaag 8 46 1 ctagtttttt 0.883217 -255 tttactgcagttagctgtttcggttttgca 8 138 0 ttagctgttt 0.942591 -163 agtcttacgactggctttttatctaaaacg 8 224 0 ctggcttttt 0.985931 -77 agtcgtaagactggttttttatttgcatta 8 242 1 ctggtttttt 0.906862 -59 ********** Masking position 8 Map Score: 14.4707 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 192 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 AAAAAATAAAGCTAGGTAACTATATTTTAA 1 18 0 GCTAGGTAAC 0.989348 -232 ATTTTTTAGAGCTAGGTACCTCATTTCATA 1 41 1 GCTAGGTACC 0.988496 -209 agttgagaaggctagggaacaccatttatt 8 74 1 gctagggaac 0.994021 -227 ********** Masking position 4 Map Score: 2.62631 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 2 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 7 ATTCGCACTTGCATTGGCAGCATTTCTTGTT 1 90 0 GCATTGCAGC 0.967238 -160 TGCGCTAAGTGCAACAGCTGCTGTAAAAAGT 1 120 1 GCAACGCTGC 0.708459 -130 tttcggttttgcaaccacagcatttcttgtc 8 120 0 gcaacacagc 0.971931 -181 cgccacagttgcatttactgcagttagctgt 8 150 0 gcattactgc 0.863 -151 ggcagcatttgcaaccgccacagttgcattt 8 165 0 gcaacgccac 0.968299 -136 ***** ***** Masking position 3 Map Score: 2.15736 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 = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 ATTTCTTGTTGTCTTCCATCACTTTAATTT 1 70 0 GTCTTCCATC 0.988731 -180 CAAAATTTTTGTCTAACAACTAAAAAGCCA 1 155 1 GTCTAACAAC 0.959369 -95 agcatttcttgtcttccatcttaatatgaa 8 103 0 gtcttccatc 0.988731 -198 agctgtttcggttttgcaaccacagcattt 8 126 0 gttttgcaac 0.927178 -175 taaaaaaccagtcttacgactggcttttta 8 233 0 gtcttacgac 0.907484 -68 ********** Masking position 4 Map Score: 3.15412 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 7 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 ********** No masking Map Score: -3.13817e-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 10 ********** No masking Map Score: -3.13817e-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: -3.13817e-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