AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_mgen_mpneu_300.orf -o020_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: 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 RMP00443 255 Mycoplasma_pneumoniae #6 RMP00444 166 Mycoplasma_pneumoniae #7 RMP00445 67 Mycoplasma_pneumoniae #8 RMP00446 20 Mycoplasma_pneumoniae #9 RMP00448 300 Mycoplasma_pneumoniae Motif number 1 AGCTAGGTAACTATATTTTAAAAAAGTG 1 7 0 CTAATTTTAA 0.891845 -243 TTACCTAGCTTTATTTTTTAGAGCTAGGTACC 1 29 1 TTATTTTTAA 0.980835 -221 AAATTTTGTCTTACTTTTTACAGCAGCTGTTG 1 131 0 TTATTTTTAA 0.980835 -119 TACTGGCTTTTTAGTTGTTAGACAAAAATTTT 1 156 0 TTATTGTTAA 0.955828 -94 CTGGCTTTTTTTATTTGTTATAGATCACTACT 1 194 1 TTATTGTTAA 0.955828 -56 TACTTAAAGTTTAAATTTAATAGTAGTGATCT 1 215 0 TTAATTTAAA 0.909458 -35 CTTAGTTTTAAATTAGCATAGAt 2 2 1 TTATTTTAAT 0.820617 -26 CAAAAGCTTAATTTTAAAAGtTCGAATCA 3 8 1 TTATTTTAAA 0.963447 -75 TTTTAATAACTTAAATTTTATATAAATATTAA 4 14 0 TTAATTTTAA 0.951225 -53 ACCTCACTAACTATTTTTAATAACTTAAATTT 4 28 0 CTATTTTAAA 0.917659 -39 ccaccactgtttattttttaaaccataagtcc 5 165 1 ttatttttaa 0.980834 -91 cgtgaaaatattaatcttaagacattgattac 7 43 1 ttatcttaaa 0.781485 -25 aattatttgttagtttaatc 8 7 0 ttattgttat 0.789716 -14 ataattgcacctagtttttttaactaaaagtt 9 46 1 ctatttttta 0.664531 -255 taaaaactgttttaattttagatttaaagcaa 9 275 0 tttattttaa 0.640973 -26 *** ****** * Masking position 8 Map Score: 20.0724 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 CAGTTTAGTTACTGGCTTTTTAGTTGTTAG 1 167 0 ACTGGCTTTT 0.995246 -83 CAGTAACTAAACTGGCTTTTTTTATTTGTT 1 183 1 ACTGGCTTTT 0.995246 -67 gtttcctttgactggctcttaaagattgga 5 32 1 actggctctt 0.987109 -224 cccctaagcgactgtcgtttagaagcttat 5 114 0 actgtcgttt 0.95604 -142 cactaccaccactgtttattttttaaacca 5 160 1 actgtttatt 0.932992 -96 tttctgtttcactgtttattatcttaaaaa 6 27 0 actgtttatt 0.932992 -140 cagtcttacgactggctttttatctaaaac 9 225 0 actggctttt 0.995246 -76 cagtcgtaagactggttttttatttgcatt 9 241 1 actggttttt 0.987934 -60 ********** Masking position 1 Map Score: 17.4996 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 25 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 3 ATATAGTTACCTAGCTTTATTTTTTAGAGC 1 23 1 CTAGCTTTAT 0.961067 -227 AATGAGGTACCTAGCTCTAAAAAATAAAGC 1 36 0 CTAGCTCTAA 0.724769 -214 AGTTTAGTTACTGGCTTTTTAGTTGTTAGA 1 166 0 CTGGCTTTTT 0.993737 -84 AGTAACTAAACTGGCTTTTTTTATTTGTTA 1 184 1 CTGGCTTTTT 0.993737 -66 tcaaaggaaacccgctttttcagtcccact 5 13 0 cccgcttttt 0.872622 -243 tttcctttgactggctcttaaagattggaa 5 33 1 ctggctctta 0.944217 -223 tatcctggtcttagcttttttgggcctgtt 5 64 1 ttagcttttt 0.938753 -192 ataattgcacctagtttttttaactaaaag 9 46 1 ctagtttttt 0.938753 -255 tttactgcagttagctgtttcggttttgca 9 138 0 ttagctgttt 0.781712 -163 agtcttacgactggctttttatctaaaacg 9 224 0 ctggcttttt 0.993737 -77 agtcgtaagactggttttttatttgcatta 9 242 1 ctggtttttt 0.960696 -59 ********** Masking position 6 Map Score: 17.3692 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 57 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 CATTCGCACTTGCATTGGCAGCATTTCTTGTT 1 90 0 TGCATGCAGC 0.995246 -160 ATGCGCTAAGTGCAACAGCTGCTGTAAAAAGT 1 119 1 TGCAAGCTGC 0.997446 -131 gaaaaaggacggcaatggcagcggtaacaata 5 229 1 ggcaagcagc 0.993047 -27 gtttcggttttgcaaccacagcatttcttgtc 9 120 0 tgcaaacagc 0.992481 -181 ccgccacagttgcatttactgcagttagctgt 9 150 0 tgcatactgc 0.986061 -151 ctgtggcggttgcaaatgctgccaaaaataag 9 173 1 tgcaagctgc 0.997446 -128 ***** ***** Masking position 4 Map Score: 11.0318 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 6 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 5 GCACTTGCATTGGCAGCATTTCTTGTTGTCTTCCAT 1 81 0 TAGCATTTTT 0.976149 -169 TTAAGGATAATTTGTGCAGTAGTGATTCGAaCTTTT 3 26 0 TTGCATATGT 0.963696 -57 ATATCTTAGCTGCAGTAATTTTTTAAGCTATT 3 61 0 TTGCATATTT 0.98406 -22 tttttgggcctgtttggaattatttttggtagttat 5 80 1 ttggattttt 0.960268 -176 cttgttagcgtccttggacttatggtttaaaaaata 5 176 0 ttggatttgt 0.91222 -80 taagtttagttaagtgcggtatttat 7 1 0 ttgcgtattt 0.927928 -67 ttaaaaaaactaggtgcaattattctaacaaacccc 9 33 0 ttgcattttt 0.989057 -268 ggttttgcaaccacagcatttcttgtcttccatctt 9 111 0 cagcattttt 0.895124 -190 actggttttttatttgcattacttttgctttaaatc 9 251 1 ttgcatattt 0.98406 -50 aaatctaaaattaaaacagtttttatatc 9 282 1 taacattttt 0.78145 -19 * **** ** ** * Masking position 10 Map Score: 7.83576 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 112 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 aCTTTTAAAATTAAGCTTTTG 3 2 0 TTAAGCTTTT 0.908143 -81 CAGTAATTTTTTAAGCTATTTAAGGATAAT 3 51 0 TTAAGCTATT 0.958475 -32 TATATAAAATTTAAGTTATTAAAAATAGTT 4 22 1 TTAAGTTATT 0.720727 -45 GTGAGGTTCAAAAAGCGCTTTTCT 4 53 1 AAAAGCGCTT 0.814097 -14 aaaaactgttaaaagcgtttc 6 2 0 aaaagcgttt 0.70981 -165 aatagctcgatcaagcgcttggagtttctg 6 51 0 tcaagcgctt 0.955776 -116 gatcgagctattaagcgatttaatgacttt 6 69 1 ttaagcgatt 0.979478 -98 aatattaatcttaagacattgattacgat 7 49 1 ttaagacatt 0.735863 -19 tcaagccatttgaaataagt 9 1 1 tcaagccatt 0.94378 -300 ********** Masking position 4 Map Score: 4.13384 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 138 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TGTTAGACAAAAATTTTGTCTTACTTTTTACAG 1 140 0 AAATTTTGTA 0.898082 -110 CTTAATTTTAAAAGtTCGAATCACTACTGCACA 3 17 1 AAAGtTCGTA 0.9275 -66 ctggctcttaaagattggaattatcctggtctt 5 43 1 aagattggta 0.951442 -213 actgtttaaaaaaattggcgtaatgtcgtaaaa 6 117 0 aaaattggta 0.952392 -50 taactaaacttagtttggcgtgaaaatattaat 7 25 1 tagtttggta 0.889838 -43 catttgaaataagtttggggtttgttagaataa 9 17 1 aagtttggtt 0.889838 -284 aaatttagagaaatttcgccttatttttggcag 9 191 0 aaatttcgta 0.972213 -110 aaatttctctaaatttcgttttagataaaaagc 9 208 1 aaatttcgta 0.97221 -93 ******** * * Masking position 2 Map Score: 3.09327 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 30 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 AAAAAATAAAGCTAGGTAACTATATTTTAA 1 18 0 GCTAGGTAAC 0.989432 -232 ATTTTTTAGAGCTAGGTACCTCATTTCATA 1 41 1 GCTAGGTACC 0.988366 -209 agttgagaaggctagggaacaccatttatt 9 74 1 gctagggaac 0.992784 -227 ********** Masking position 4 Map Score: 1.89896 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 9 CAGCATTTCTTGTTGTCTTCCATCACTTTAATT 1 71 0 TTTGTCTTCT 0.977325 -179 TAGACAAAAATTTTGTCTTACTTTTTACAGCAG 1 137 0 TTTGTCTTAT 0.981128 -113 ccacagcatttcttgtcttccatcttaatatga 9 104 0 tttgtcttct 0.977325 -197 tttagagaaatttcgccttatttttggcagcat 9 188 0 ttcgccttat 0.972776 -113 tttctctaaatttcgttttagataaaaagccag 9 211 1 ttcgttttat 0.935749 -90 tttgcattacttttgctttaaatctaaaattaa 9 263 1 tttgctttat 0.935748 -38 * ******** * Masking position 8 Map Score: 1.28877 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 11 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 10 ACAACAAGAAATGCTGCCAATGCAAGTGCG 1 88 1 ATGCTGCCAA 0.964901 -162 aagtccaaggacgctaacaaggagttagat 5 191 1 acgctaacaa 0.970728 -65 tccagtacaaactcaaacaattcactgttt 6 143 0 actcaaacaa 0.857307 -24 aggtgcaattattctaacaaaccccaaact 9 28 0 attctaacaa 0.931129 -273 gcggttgcaaatgctgccaaaaataaggcg 9 178 1 atgctgccaa 0.964901 -123 agcaaaagtaatgcaaataaaaaaccagtc 9 250 0 atgcaaataa 0.768406 -51 ********** Masking position 9 Map Score: 1.12234 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 55 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 ttttgggcctgtttggaattatttttggta 5 81 1 gtttggaatt 0.863624 -175 agcgcttggagtttctgtttcactgtttat 6 38 0 gtttctgttt 0.935186 -129 acagtgaattgtttgagtttgtactggaac 6 145 1 gtttgagttt 0.954581 -22 tttgaaataagtttggggtttgttagaata 9 19 1 gtttggggtt 0.979992 -282 gcagttagctgtttcggttttgcaaccaca 9 132 0 gtttcggttt 0.982855 -169 ********** Masking position 4 Map Score: 0.944965 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 28 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 TGCCAATGCAAGTGCGAATGCGCTAAGTGC 1 102 1 AGTGCGAATG 0.958939 -148 GAATGCGCTAAGTGCAACAGCTGCTGTAAA 1 117 1 AGTGCAACAG 0.986091 -133 ccagtgggactgaaaaagcggg 5 3 1 agtgggactg 0.988455 -253 cagtggtggtagtggaaccgttgaacacta 5 144 0 agtggaaccg 0.976518 -112 gataataaacagtgaaacagaaactccaag 6 34 1 agtgaaacag 0.946933 -133 ggattcccggagtgggaaagtcattaaatc 6 85 0 agtgggaaag 0.958941 -82 aactgcagtaaatgcaactgtggcggttgc 9 156 1 aatgcaactg 0.901922 -145 ********** Masking position 7 Map Score: 8.09006 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 6 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 ********** No masking Map Score: -2.10077e-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 14 ********** No masking Map Score: -2.10077e-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 15 ********** No masking Map Score: -2.10077e-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