AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mgen_mpneu_300.orf -o293_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 Input sequences: #1 RMG00022 300 Mycoplasma #2 RMG01110 46 Mycoplasma #3 RMG00025 65 Mycoplasma #4 RMG02159 188 Mycoplasma #5 RMG01114 41 Mycoplasma #6 RMG00035 29 Mycoplasma #7 RMG02168 26 Mycoplasma #8 RMG04109 85 Mycoplasma #9 RMG02265 300 Mycoplasma #10 RMG01247 55 Mycoplasma #11 RMG00170 20 Mycoplasma #12 RMG05352 177 Mycoplasma #13 RMG04246 172 Mycoplasma #14 RMP00131 20 Mycoplasma_pneumoniae #15 RMP00134 45 Mycoplasma_pneumoniae #16 RMP00137 300 Mycoplasma_pneumoniae #17 RMP00170 170 Mycoplasma_pneumoniae #18 RMP00172 180 Mycoplasma_pneumoniae #19 RMP00613 55 Mycoplasma_pneumoniae #20 RMP00617 275 Mycoplasma_pneumoniae Motif number 1 GTTCAAGTCCATTTACTTCCACCAATAATGGGGATGTAG 1 116 0 ATTTTAAAAT 0.915073 -185 TCGAGGGGTATTTTGGTTAAATTAAAATTGTTATAATAA 1 236 0 TTTTTAAAAT 0.975652 -65 AAATTAGCTGTTTTGATTATAAAAACTGTTAAAATTCGA 1 271 0 TTTTTAAATT 0.964488 -30 ATTAATAATGTTtGTCTTTCAACACTATTAAATTTAT 3 9 0 TTtGTAACAT 0.7794 -57 AACCGTTTACTTTTTTATGAACAAGCACTACAAAGGTTT 4 37 1 TTTTTAAGAT 0.853913 -152 AGTGTTTTGCTTTTAGATAAACTAAAAATAACGTGCTTT 8 14 0 TTTTTAAAAT 0.975652 -72 TTCTTTTTTTATTTCTATTTAGTAAATGTTCAAGTATAT 9 208 1 ATTTTAAATT 0.879547 -93 GTTTTTTTGGTTTGAACTACATTAACTGTAATTATACTG 12 124 0 TTTGTAAATT 0.942583 -54 AATAAGGATATTTGAAGTCAAAAAACTGTTGCCTGAATT 13 77 1 TTTGTAAATT 0.942583 -96 ACAGTGTTGTTTTGTAATCCAAAAAAAGTAAATTCAGGC 13 107 0 TTTGTAAAAT 0.960343 -66 atcgaaaccgatttaattatattaatacttcgcttggac 16 234 0 attttaaaat 0.915073 -67 tttttgatgaacgaaattaatattctggc 16 282 0 tttttaaata 0.713162 -19 tggcagcaggttttatttagatcaaatctcaattgggaa 17 71 0 tttttaaatt 0.964488 -100 atttgactggtttttattctaacaacactaagggtaact 18 132 0 tttttaaaat 0.975648 -49 tattttttctttttccttggaccaagagtccagggagtc 20 190 0 tttttaaaat 0.975652 -86 **** * * ** * * Masking position 11 Map Score: 16.9484 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 95 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 TTGATTATAAAAACTGTTAAAATTCGAGGGGT 1 266 0 AAACTTAAAA 0.473863 -35 TTTATAATCAAAACAGCTAATTTT 1 287 1 AAACATAATT 0.800291 -14 CTCAAAAAACTAATACATCAAACTT 4 4 1 AAAAATAATA 0.856183 -185 AACAGTTTTAAAAAGCGCAATTTGATTCTTAT 4 134 0 AAAAGCAATT 0.866586 -55 AGCAAGAATTATAATTAACACTCTAA 5 5 1 AGAATTAATT 0.800291 -37 AAATCAATAAAATTCTAATACTACTTTTC 6 10 0 AAAATTAATA 0.856183 -20 AAATATCTGCAAAAAACTAAATATTTCAGAGG 8 59 1 AAAAATAAAT 0.856183 -27 GCTGTGGTACAAACGCTTAATTAGCTCCCACA 10 29 0 AAACGTAATT 0.822759 -27 ACCAACGCATAAAATTTTAATATCTGTT 12 7 0 AAAATTAATA 0.856183 -171 ATGTTTACTTAAAAGTGCAATAAAAGCCTTGA 12 39 0 AAAAGCAATA 0.754864 -139 AAGTAAACATAAAAAGATAATTTTCGTCACTT 12 61 1 AAAAATAATT 0.92624 -117 TTCAAACCAAAAAAACCCAAATCGGTCAAAAA 12 147 1 AAAAACAAAT 0.726649 -31 TTGTAATCCAAAAAAAGTAAATTCAGGCAACA 13 103 0 AAAAATAAAT 0.856183 -70 tagtttcgtcaaaatattaattgtgagcttac 15 11 1 aaaattaatt 0.926241 -35 aaaattcgccagaatattaatttcgttcatca 16 275 1 agaattaatt 0.800291 -26 agggggtggcaaaagtataattaacagatacc 17 146 1 aaaagtaatt 0.935677 -25 accatcgcataaaattctaaatagcgcgac 18 9 0 aaaattaaat 0.856183 -172 tccctggtaaaaaagcacaaaaaaatcatctt 18 55 1 aaaagcaaaa 0.593474 -126 agccaaagttagaaaggtaattaagatgattt 18 77 0 agaaataatt 0.800291 -104 ***** ***** Masking position 9 Map Score: 15.0923 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 267 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 TTTTGATCAGCTAAATAAAACAAAGCAA 3 48 1 CTAATAAAAC 0.924101 -18 TGAAATAATTCTTCATAAAACCTTTGTAGTG 4 62 0 CTCATAAAAC 0.951019 -127 TTTAGATAAACTAAAAATAACGTGCTTTTTA 8 11 0 CTAAAATAAC 0.924101 -75 TTGAAAATATCTGCAAAAAACTAAATATTTC 8 55 1 CTCAAAAAAC 0.979898 -31 CCAGTACCATTTCCAAAAAACTGAGAACCTG 9 166 1 TTCAAAAAAC 0.882488 -135 AACTGAGAACCTGAAAAAAACAGGTTCTTTT 9 184 1 CTAAAAAAAC 0.968322 -117 AGTTTTTTGACTTCAAATATCCTTATTTAGA 13 73 0 CTCAAATATC 0.828107 -100 TATCGCTCATCTTTAAATAACAGTGTTGTTT 13 134 0 CTTAAATAAC 0.750231 -39 gagatttgatctaaataaaacctgctgccaa 17 80 1 ctaataaaac 0.924101 -91 atgttgagagctaaaaaagacaaagcttggc 17 106 0 ctaaaaagac 0.851993 -65 ttggtgattgttacaaaaatcgctgatttta 20 47 1 ttcaaaaatc 0.650757 -229 ** ******** Masking position 5 Map Score: 9.45142 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 92 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 ACATTATTAATTTTTGATCAGCTAAATAAA 3 37 1 TTTTTGATCA 0.955326 -29 AACCGTTTACTTTTTTATGAACAAGCACTA 4 37 1 TTTTTTATGA 0.857829 -152 TTTAAAACTGTTTTTGATGATTACAAAACC 4 154 1 TTTTTGATGA 0.955326 -35 TTAGTATCATTTTTTTATAAAATAATCAAG 9 13 1 TTTTTTATAA 0.670921 -288 CCTTTTTGATAGTTTTTTCA 11 9 0 TTTTTGATAG 0.837262 -12 CTATGTTAGTTTTTGACCGATTTGGGTTT 12 159 0 TTTTTGACCG 0.915547 -19 cacaattaatattttgacgaaacta 15 6 0 attttgacga 0.681773 -40 ttctggcgaatttttgatcgaaaccgattt 16 259 0 tttttgatcg 0.93837 -42 tttttgatgaacgaaattaa 16 291 0 tttttgatga 0.955326 -10 ttttttgtgcttttttaccagggaaaccaa 18 49 0 ttttttacca 0.811181 -132 ********** Masking position 5 Map Score: 7.90365 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 102 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 5 ATTCGAGGGGTATTTTGGTTAAATTAAAAT 1 247 0 TATTTTGGTT 0.807375 -54 AAAATTAGCTGTTTTGATTATAAAAACTG 1 282 0 TGTTTTGATT 0.771101 -19 TTGCTTTGTTTTATTTAGCTG 3 55 0 TGCTTTGTTT 0.90054 -11 TTTCAACCAGTGTTTTGCTTTTAGATAAAC 8 31 0 TGTTTTGCTT 0.833135 -55 ACTAAATTTATGTTTGGTTTCAAATGAAGT 9 66 1 TGTTTGGTTT 0.682913 -235 TAGCAGTAGTTGCGATGTTTATCGTAATGT 9 264 1 TGCGATGTTT 0.821433 -37 TAAAATTTTATGCGTTGGTTCAAGGCTTTT 12 20 1 TGCGTTGGTT 0.960491 -158 AAAATTATCTTTTTATGTTTACTTAAAAGT 12 55 0 TTTTATGTTT 0.442313 -123 CGATTTGGGTTTTTTTGGTTTGAACTACAT 12 141 0 TTTTTTGGTT 0.807375 -37 ACTTCAATTTTATTTTGGTTCACTTTAATA 13 31 1 TATTTTGGTT 0.807375 -142 TTTAAATAACAGTGTTGTTTTGTAATCCAA 13 124 0 AGTGTTGTTT 0.620257 -49 tagaattttatgcgatggtttagtgtgttg 18 22 1 tgcgatggtt 0.910417 -159 gatggtttagtgtgttggtttccctggtaa 18 35 1 tgtgttggtt 0.973449 -146 gcgattgtgacggtttgggtttgca 20 261 0 tgtgacggtt 0.707379 -15 ********** Masking position 9 Map Score: 7.60966 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 207 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TTAAATACCCTTAGGATTATGCTTGGAAGTATAG 1 198 0 TTAATATCTT 0.956826 -103 TAAATTAAAATTGTTATAATAATTAGTTAAATAC 1 224 0 TTGATATATT 0.880973 -77 AATAATCTATTTGAAATAATTCTTCATAAAACCT 4 70 0 TTGATATCTT 0.957597 -119 CTTAGAGTGTTAATTATAATTCTTGCT 5 4 0 TAAATATCTT 0.702244 -38 TATTAGTATCATTTTTTTATAAAATA 9 3 1 TTAATATTTT 0.904378 -298 TCCTGCTTTATTGTAATCATGCTTTAGATTTAGA 9 107 1 TTGATATCTT 0.957597 -194 TCCTAATCGTTTAAGAATATACTTGAACATTTAC 9 229 0 TTAAAATCTT 0.719651 -72 TTCATTACCATTGGCAGTATAATTACAGTTAATG 12 110 1 TTGAGATATT 0.559589 -68 ATGAGCGATATTATAATTATTTGTAACA 13 155 1 TTAATATTGT 0.598673 -18 accgatttaattatattaatacttcgcttggaca 16 233 0 ttattatctt 0.702243 -68 agaaaggtaattaagatgatttttttgtgctttt 18 65 0 ttaatatttt 0.904378 -116 agatgtttttttgctatgatcattcatg 20 5 0 ttgatatatt 0.880973 -271 ttgtgaaagcttatgattattttttctttttcct 20 212 0 ttaatatttt 0.904378 -64 *** ** ** *** Masking position 9 Map Score: 8.17513 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 68 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 7 TTAAAGAATTCCAACGTCTAACTTACCTTTG 1 19 0 CCAACGCTAA 0.970756 -282 ACAAAAGTAACCAGCTTCTAAATCTAAAGCA 9 126 0 CCAGCTCTAA 0.970756 -175 AAGCCTTGAACCAACGCATAAAATTTTAATA 12 17 0 CCAACGATAA 0.928447 -161 cgtgagtcctccaactcccaaactctgggaa 16 71 0 ccaactccaa 0.977579 -230 tattcccactccagctaccaagttcaggtaa 16 152 0 ccagctccaa 0.981362 -149 ctaaataaaacctgctgccaagctttgtctt 17 90 1 cctgctccaa 0.904175 -81 acacactaaaccatcgcataaaattctaaat 18 19 0 ccatcgataa 0.79773 -162 gtcaaatcacccaacaaacaacaacaa 18 164 1 ccaacaacaa 0.838193 -17 ****** **** Masking position 10 Map Score: 4.83075 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 21 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 AGTTGAGCTACATCCCCATTATTGGTGGAA 1 109 1 CATCCCCATT 0.965788 -192 GAACCATCGACCTCACCCTTATCAGGGGTG 1 151 1 CCTCACCCTT 0.932427 -150 GTTtGTCTTTCAACACTATTAAATTTAT 3 9 0 CAACACTATT 0.770388 -57 GATTTGAAAACATTCCCATTAAAGATAAGA 4 110 1 CATTCCCATT 0.916907 -79 TTGATGATTACAAAACCATTGATTTAGCAG 4 167 1 CAAAACCATT 0.841134 -22 TTCAGGTAACCAGTACCATTTCCAAAAAAC 9 157 1 CAGTACCATT 0.857682 -144 TTATTAGTTTCATTACCATTGGCAGTATAA 12 102 1 CATTACCATT 0.930449 -76 tatacttttgccacccccttttccttttat 17 135 0 ccaccccctt 0.919236 -36 ttaaccacaccattattgcgattt 19 42 0 ccacaccatt 0.965788 -14 ********** Masking position 9 Map Score: 5.08609 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 56 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 TGTAAAACCAAGTTCTTGAA 2 1 1 TGTAAAACCA 0.877072 -46 TTTTGATGATTACAAAACCATTGATTTAGC 4 165 1 TACAAAACCA 0.948945 -24 GTTAATGTAGTTCAAACCAAAAAAACCCAA 12 137 1 TTCAAACCAA 0.811357 -41 TTTTTTGGATTACAAAACAACACTGTTATT 13 120 1 TACAAAACAA 0.862646 -53 ctgatcaatctgcaaacctagaaattacca 16 34 1 tgcaaaccta 0.92716 -267 cacccactgctgcaaaaccagccaaagtta 18 98 0 tgcaaaacca 0.982145 -83 tataagaatttgcaaacccaaaccgtcaca 20 251 1 tgcaaaccca 0.985169 -25 ********** Masking position 5 Map Score: 4.6228 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 58 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 10 GGTTTGAGACCCTTCATCTCCACCATTAAAG 1 44 0 CCTTATCTCC 0.891397 -257 GGTCTCAAACCCTCAACCTCCTGAGTGCAAA 1 64 1 CCTCACCTCC 0.993672 -237 GGTTCAAGTCCATTTACTTCCACCAATAATG 1 125 0 CATTACTTCC 0.849793 -176 GGACTTGAACCATCGACCTCACCCTTATCAG 1 145 1 CATCACCTCA 0.907928 -156 AAAACTAATACATCAAACTTCAACCGTTTAC 4 16 1 CATCAACTTC 0.769162 -173 gaaattaccacctctacttcccagagtttgg 16 54 1 cctcacttcc 0.977186 -247 aaacgtgagtcctccaactcccaaactctgg 16 74 0 cctcaactcc 0.981501 -227 **** ****** Masking position 6 Map Score: 2.55891 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 9 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 CAACTGATAGAGCACCTGATTTGCACTCAGG 1 83 0 AGCACCTGTT 0.933598 -218 AAATCTTTCAAGAACTTGGTTTTACA 2 6 0 AGAACTTGTT 0.923707 -41 GTTGGATTATAAATCCTGCTTTATTGTAATC 9 94 1 AAATCCTGTT 0.856746 -207 CTTTAGATTTAGAAGCTGGTTACTTTTGTTT 9 128 1 AGAAGCTGTT 0.910526 -173 AAATAAAAAAAGAACCTGTTTTTTTCAGGTT 9 191 0 AGAACCTGTT 0.981459 -110 TTTGAAGTCAAAAAACTGTTGCCTGAATTTA 13 87 1 AAAAACTGTG 0.809265 -86 tgatctaaataaaacctgctgccaagctttg 17 86 1 aaaacctgtg 0.970336 -85 aacatcttacaaaacttggtgattgttacaa 20 32 1 aaaacttgtg 0.882102 -244 ******** ** Masking position 1 Map Score: 2.69807 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 65 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 AACTGATAGAGCACCTGATTTGCACTCAGG 1 83 0 GCACCTGATT 0.803104 -218 GAAGTATAGCTCAGTTGGTTAGAGCACACC 1 177 0 TCAGTTGGTT 0.736588 -124 AATCTTTCAAGAACTTGGTTTTACA 2 6 0 GAACTTGGTT 0.965419 -41 GGTTTCAAATGAAGTTGGATTATAAATCCT 9 81 1 GAAGTTGGAT 0.844996 -220 TTTAGATTTAGAAGCTGGTTACTTTTGTTT 9 129 1 GAAGCTGGTT 0.982095 -172 AATAAAAAAAGAACCTGTTTTTTTCAGGTT 9 191 0 GAACCTGTTT 0.831785 -110 tcaggtaaatgaaggtggttattaccccta 16 130 0 gaaggtggtt 0.93968 -171 tcatttacctgaacttggtagctggagtgg 16 148 1 gaacttggta 0.814848 -153 acaaagcttggcagcaggttttatttagat 17 88 0 gcagcaggtt 0.877032 -83 ********** Masking position 3 Map Score: 2.55327 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 58 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 ********** No masking Map Score: -6.52746e-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: -6.52746e-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: -6.52746e-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