AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_mgen_mpneu_300.orf -o215_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 RMG00426 270 Mycoplasma #2 RMG01505 45 Mycoplasma #3 RMG02531 69 Mycoplasma #4 RMG00446 18 Mycoplasma #5 RMG02541 92 Mycoplasma #6 RMG05457 300 Mycoplasma #7 RMP00268 300 Mycoplasma_pneumoniae #8 RMP00269 187 Mycoplasma_pneumoniae #9 RMP00272 103 Mycoplasma_pneumoniae #10 RMP00274 121 Mycoplasma_pneumoniae #11 RMP00276 99 Mycoplasma_pneumoniae #12 RMP00278 169 Mycoplasma_pneumoniae #13 RMP00279 213 Mycoplasma_pneumoniae #14 RMP00280 203 Mycoplasma_pneumoniae #15 RMP00512 146 Mycoplasma_pneumoniae #16 RMP00513 23 Mycoplasma_pneumoniae #17 RMP00517 300 Mycoplasma_pneumoniae Motif number 1 ATAACTCCTTTTGTCTATTAATCACATCTAAATCTAAAAG 1 9 1 TTTTAAAATA 0.87138 -262 AATTAACCCTTGATAAACTACAAAACAATAAAAAAGCCTACC 1 185 0 TGATTAAAAA 0.367119 -86 AATGTTTATTAAAAAAACAAAATAAAAAGCGGTTTT 3 5 1 TTTAAAAAAA 0.883412 -65 TAAGATAGTTTTAAAACAAGTAATTCTAACAAATTCTAACTG 5 20 0 TTAAAAAAAA 0.723034 -73 AATAGTaCTTTTTTTATCAGGAATAATACCAATGGCTTGAAA 6 20 1 TTTTAAAAAA 0.969866 -281 ACTTCGATTTTTTTTAGTTCTAATAACATTAATGCTAAGTTT 6 77 1 TTTTTAAAAA 0.807494 -224 GTTAGTCATTTTATTCAAAAGAAAAAAACTTAGCATTAATGT 6 102 0 TTATAAAATA 0.701891 -199 GCAGAAATCGTTTTTAAAATAAAGAAAAAGAAACCAAAATA 6 270 1 TTTTAAAAAA 0.969777 -31 ccaattaattttttagggtttaaaagaaattagcattaggct 7 48 1 tttttaaata 0.514617 -253 gcttaaaaagtttcaacaataaaaactaaaaactctacgcca 7 121 0 tttcaaaaaa 0.772611 -180 ggttaggaaatttaattgaaaaactaccacaaacttttcaac 7 174 0 tttaaaacaa 0.806953 -127 ttagttttaattactaaccacatatacaaggttgag 8 5 1 ttttaaaata 0.87232 -183 gattaagcgtttattgccaataaggcactcaaccttgtatat 8 32 0 ttataaacaa 0.859526 -156 agcttcaaagtttttgccaaaaaagcgcttaaacaagtagtt 10 21 0 ttttaaacaa 0.946627 -101 aaaattttaatttttaatattaatataacgaactttatagcg 11 20 0 ttttaaaaaa 0.919706 -80 cacacaatgatgtagtagacaaagaccaaaaagaagctaaag 12 71 0 tgtaaaaaaa 0.718378 -99 taaacaaaaattattaaaagcaagcgtctcaaactatcaggt 13 136 0 ttataaacaa 0.859546 -78 tcaagctgctttttaattaataaacttactaacctggtttta 14 125 1 ttttaaaaaa 0.969837 -79 actaacctggttttaataaccaacataagcaatacgaaaatt 14 152 1 ttttaaaaaa 0.969875 -52 ccgatctgaatgatatacataaatatacataat 15 2 0 tgataaacaa 0.673169 -145 aaagttattttggcaaagaaaaccataaaacatatttgt 15 118 0 ttttaaaaaa 0.969772 -29 aactcgacgattttgccgaaaaatcacagaatattcgcgaat 17 78 1 ttttaaaaat 0.644039 -223 aacccccgaatgttcgccaataattgtaacaaaattgtccaa 17 179 1 tgttaaaaaa 0.915516 -122 aatttgcggaaaaaaatttcgaaatattcgaaat 17 277 0 tttgaaacaa 0.653145 -24 **** * ** * ** Masking position 1 Map Score: 26.9818 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 352 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 TTAAGATAGTTTTAAAACAAGTAATTCTAAC 5 32 0 TTTAAAAAAG 0.495721 -61 AGTCATTTTATTCAAAAGAAAAAAACTTAGC 6 110 0 TTCAAAAAAA 0.729488 -191 AGAAATCGTTTTTAAAATAAAGAAAAAGAAA 6 272 1 TTTAAAAAAA 0.82643 -29 ttttttagggtttaaaagaaattagcattag 7 56 1 tttaaaaaaa 0.826367 -245 tatttgttatttccaaacaaatatttttc 7 282 1 ttccaaaaaa 0.901934 -19 taagcgtttattgccaataaggcactcaacc 8 40 0 ttgccaaaag 0.832845 -148 aatgcttaaagtgcaaataaaaataatttag 8 128 0 gtgcaaaaaa 0.954513 -60 tgaggctaaggtgccaataaaaaaagggctg 9 53 0 gtgccaaaaa 0.915095 -51 ttcaaagtttttgccaaaaaagcgcttaaac 10 29 0 ttgccaaaaa 0.960218 -93 ctttaataatttgcaaacaaagctcgatgcc 10 63 0 ttgcaaaaaa 0.979164 -59 caaattctggttgaaaagaaagctgcaagct 10 96 0 ttgaaaaaaa 0.932335 -26 ctggagaaaatggcaaataaactaatccagc 13 38 0 tggcaaaaaa 0.906547 -176 ttaagttagctttcaaaaaaagcatgttggt 14 16 1 tttcaaaaaa 0.942 -188 acatgagattgttcaaacaaagagcagctat 14 95 0 gttcaaaaaa 0.878823 -109 caatattaaagtgcgaataaacgcagaagac 15 73 1 gtgcgaaaaa 0.849246 -74 acgccaaggatttaaaacaaatatgttttat 15 102 1 tttaaaaaaa 0.826455 -45 aaagttattttggcaaagaaaaccataaaac 15 126 0 tggcaaaaaa 0.906547 -21 ctcgacgattttgccgaaaaatcacagaata 17 80 1 ttgccgaaaa 0.832845 -221 aatttgcggaaaaaaatttcgaaa 17 287 0 ttgcggaaaa 0.722545 -14 ******* *** Masking position 7 Map Score: 21.9644 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 289 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 CTTTATTTGCCTATCAGTTAAATAACTGGTAG 1 158 1 CTACATTAAA 0.856885 -113 AATGAAATGACTACAACTTAAATTAACCCTTG 1 215 0 CTAAATTAAA 0.878918 -56 TTTTATCTTAGCATAAAAATTTCTTTTTG 1 252 0 TTACAAAAAA 0.655838 -19 CAATTCTAAACGATAAATTAAATTAA 2 5 0 CGAAATTAAA 0.776175 -41 AATGTTTATTAAAAAAACAAAATAAAA 3 6 1 TTATAAAAAA 0.773162 -64 ATCTTAATCCCTAATATATAAATTAGAAAGGC 5 56 1 CTATAATAAA 0.845899 -37 ATTAATGTTATTAGAACTAAAAAAAATCGAAG 6 78 0 TTAAATAAAA 0.818415 -223 TATTTTGATCTGATTAAAAAAAAGTTAGTCAT 6 135 0 TGATAAAAAA 0.619544 -166 ACAGGTAAATCTAAAACTAAAAATCGACAAAA 6 198 1 CTAAATAAAA 0.878918 -103 agcattaggcttaaaaattaaattttcctgtt 7 79 1 ttaaattaaa 0.818397 -222 gtatatgtggttagtaattaaaactaa 8 6 0 ttatattaaa 0.869279 -182 gcttaatctactagtaaataaatcaggcacgc 8 66 1 ctataataaa 0.845913 -122 ttattaacaattagcagttaaatgcttaaagt 8 147 0 ttacattaaa 0.788028 -41 gttcgttatattaatattaaaaattaaaattt 11 29 1 ttatataaaa 0.868704 -71 aggcgttttgcgattaataaaattttaatttt 11 48 0 cgatataaaa 0.836507 -52 taatccagcactaatacaaaaactgacaataa 13 15 0 ctataaaaaa 0.845913 -199 gttagtaagtttattaattaaaaagcagcttg 14 126 0 ttatattaaa 0.86927 -78 ataagcaatacgaaaattaaaaccaagcgagc 14 176 1 cgaaataaaa 0.776175 -28 *** ** ***** Masking position 6 Map Score: 15.8667 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 152 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 GATAAACTACAAAACAATAAAAAAGCCTACCAGT 1 182 0 AAAAAAAAAA 0.95538 -89 GTTTATTAAAAAAACAAAATAAAAAGCGGTTTTA 3 14 1 AAAAAAAAAA 0.95538 -56 CTATTAAAGCAGTTAGAATTTGTTAGAA 5 5 1 TAAACAAGAA 0.664928 -88 TATTCAAAAGAAAAAAACTTAGCATTAATGTTAT 6 99 0 AAAAAAAGCA 0.913927 -202 AATCGTTTTTAAAATAAAGAAAAAGAAACCAAAA 6 275 1 AAAAAAAAAA 0.95538 -26 tttagggtttaaaagaaattagcattaggcttaa 7 59 1 aaaaaaagca 0.913927 -242 agtttcaacaataaaaactaaaaactctacgcca 7 121 0 ataaaaaaaa 0.763627 -180 acaaatacttaaaacaactaaaaaaccaatgctg 7 255 0 aaaaaaaaaa 0.95538 -46 agtgcaaataaaaataatttagcaacactaccga 8 116 0 aaaaaaagca 0.913927 -72 caggctttcaataagcagataaaagaagggttgt 9 12 1 ataacaaaaa 0.689662 -92 acaaagaccaaaaagaagctaaagctcccggtta 12 61 0 aaaaaaaaag 0.71822 -109 ctgtgttaataaaacactggagaaaatggcaaat 13 51 0 aaaaacagaa 0.694755 -163 aactgaattttaaataaacaaaaattattaaaag 13 158 0 taaaaaaaaa 0.763627 -56 tttggcaaagaaaaccataaaacatatttgtttt 15 115 0 aaaacaaaca 0.891062 -32 gcgacttacgaaaaacataaaaaacagaataccg 17 12 0 aaaacaaaaa 0.936422 -289 attttgccgaaaaatcacagaatattcgcgaatc 17 87 1 aaaacaaata 0.610499 -214 aatttgcggaaaaaaatttcgaaatattcgaaa 17 278 0 aaaaaacgaa 0.694755 -23 **** ** **** Masking position 4 Map Score: 13.5824 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 245 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 TTTTAAAACAAGTAATTCTAACAAATTCTAACTGCTT 5 17 0 ATATAAAATT 0.835279 -76 TAGTTCTAATAACATTAATGCTAAGTTTTTTTCTTTT 6 91 1 ACATGCAATT 0.888718 -210 TTTTCTTTTGAATAAAATGACTAACTTTTTTTTAATC 6 119 1 ATAAACAATT 0.730496 -182 ATTTTCAGCAATTATTATTGCATATTTTGATCTGATT 6 152 0 ATATGCTATT 0.734181 -149 AAAAATCGACAAAAGTTGCAACAAATTCAAAGTGATC 6 216 1 AAATAAAATT 0.83528 -85 atttaattgaaaaactaccacaaacttttcaacaccc 7 170 0 aaatacaatt 0.962222 -131 acactaccgaaatagtgctgctaaattagcgtgcctg 8 89 0 atatgcaatt 0.962864 -99 gcactatttcggtagtgttgctaaattatttttattt 8 108 1 gtatgcaatt 0.803677 -80 aatttttaatattaatataacgaactttatagcgcta 11 17 0 atatacaatt 0.962222 -83 cactaatacaaaaactgacaataagtta 13 2 0 aaataaaatt 0.835279 -212 atgttcgccaataattgtaacaaaattgtccaataat 17 188 1 aaatacaatt 0.961913 -113 aaattgtccaataattgtaacaaaattttccgaggta 17 210 1 aaatacaatt 0.961913 -91 taaaaacgtcacaattttggcgaaatttcgaatattt 17 253 1 aaatgcaatt 0.962899 -48 * ** * ** ** ** Masking position 4 Map Score: 8.93198 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 58 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 AATTTATATATTAGGGATTAAGATAGTTTTA 5 49 0 TTAGGATTAA 0.855606 -44 aattaattttttagggtttaaaagaaattag 7 50 1 ttaggtttaa 0.959802 -251 gaaattagcattaggcttaaaaattaaattt 7 73 1 ttaggttaaa 0.770671 -228 tgaaactttttaagcctttaatgggtgttga 7 148 1 taagctttaa 0.888595 -153 atttgcactttaagcatttaactgctaattg 8 141 1 taagctttaa 0.888595 -47 cttgaggcgttttgcgattaataaaatttta 11 53 0 tttgcattaa 0.664325 -47 aattaatgccttaggttttaactttgtcatt 12 128 1 ttaggtttaa 0.959802 -42 gtttgagacgcttgcttttaataatttttgt 13 144 1 cttgctttaa 0.833214 -70 ccaaattaagttagctttcaaaaaaagcatg 14 11 1 ttagcttcaa 0.806807 -193 gttgagctcgcttggttttaattttcgtatt 14 182 0 cttggtttaa 0.856287 -22 cagaagacgccaaggatttaaaacaaatatg 15 96 1 caaggtttaa 0.856287 -51 ***** ***** Masking position 10 Map Score: 6.38624 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 95 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 CTATTAAAGCAGTTAGAATTTGTT 5 4 1 TTAAAGCATT 0.859492 -89 ATTCAACTATTTCAAGCCATTGGTATTATTC 6 40 0 TTCAAGCCTT 0.898852 -261 TTTAAGAGATTTTCAGCAATTATTATTGCAT 6 166 0 TTTCAGCATT 0.860037 -135 gttgaaactttttaagcctttaatgggtgtt 7 146 1 tttaagcctt 0.966533 -155 ttttagttgttttaagtatttgttatttcca 7 266 1 tttaagtatt 0.698941 -35 ttactagtagattaagcgtttattgccaata 8 52 0 attaagcgtt 0.785848 -136 ttatttgcactttaagcatttaactgctaat 8 139 1 tttaagcatt 0.967175 -49 taactacttgtttaagcgcttttttggcaaa 10 20 1 tttaagcgtt 0.966533 -102 actaaatgccttgaggcgttttgcgattaat 11 62 0 ttgaggcgtt 0.817722 -38 cttggagcagttttttcaatca 12 2 1 ttggagcatt 0.835213 -168 ttaccattctttgaagccatttgaaggcgtt 13 102 1 ttgaagcctt 0.959713 -112 ******** ** Masking position 2 Map Score: 6.07539 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 126 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 AGAATTGCTATCTTAAGCAATAGTTT 2 30 1 TCTAAGCATA 0.704572 -16 AAAAGAAAAAAACTTAGCATTAATGTTATTAG 6 96 0 AATTAGCATA 0.957622 -205 AATCAGATCAAAATATGCAATAATAATTGCTG 6 152 1 AATATGCATA 0.743021 -149 ggtttaaaagaaattagcattaggcttaaaaa 7 64 1 aattagcata 0.957622 -237 caggcacgctaatttagcagcactatttcggt 8 89 1 aattagcaca 0.949081 -99 aaataaaaataatttagcaacactaccgaaat 8 113 0 aattagcaca 0.949081 -75 ttttattggcaccttagcctcattgggtcatt 9 62 1 acttagccca 0.782233 -42 ttaataaccaacataagcaatacgaaaattaa 14 164 1 actaagcata 0.937999 -40 aatcgtccccaattaaacaatattaaagtgcg 15 56 1 aataaacata 0.642614 -91 ** ****** ** Masking position 4 Map Score: 1.76046 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 50 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 9 TGACGCCATTAACTTTATTTGCCTATCAGT 1 146 1 AACTTTATTT 0.924749 -125 AAATGACTACAACTTAAATTAACCCTTGAT 1 213 0 AACTTAAATT 0.584136 -58 TTAATTTAATTTATCGTTTAGA 2 3 1 AATTTAATTT 0.6153 -43 ACTTTAATAGTaCTTTTTTTATCAGGAATA 6 15 1 TaCTTTTTTT 0.55254 -286 CATTAATGCTAAGTTTTTTTCTTTTGAATA 6 103 1 AAGTTTTTTT 0.770347 -198 TAAAATGACTAACTTTTTTTTAATCAGATC 6 131 1 AACTTTTTTT 0.926148 -170 ataacaggaaaatttaatttttaagcctaa 7 83 0 aatttaattt 0.6153 -218 tagtgttgctaaattatttttatttgcact 8 120 1 aaattatttt 0.700673 -68 taacttattgtcagtttttgt 13 2 1 aacttattgt 0.706746 -212 ttgctttaataactgaattttaaataaaca 13 172 0 aactgaattt 0.705025 -42 aaaactttatttacctctgctg 13 202 0 aactttattt 0.924749 -12 tttgaaagctaacttaatttgg 14 3 0 aacttaattt 0.887765 -201 aaagttattttggcaaagaaa 15 136 0 aagttatttt 0.814267 -11 gaatatttcgaaatttttttccgcaaatt 17 282 1 aaattttttt 0.683449 -19 ********** Masking position 2 Map Score: 8.28754 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 178 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 CAAAATAAAAAGCGGTTTTATACAATGTATAACC 3 28 1 AGCGTTTTTA 0.935734 -42 ACAATGTATAACCTGTCTAAAAGACAATTTC 3 49 1 ACCGTCTAAA 0.695695 -21 TTAGAAAGGCAACGGTTTTGAGAAG 5 78 1 AACGTTTTAA 0.930663 -15 TTTTAGATTTACCTGTCTTTAAGAGATTTTCAGC 6 180 0 ACCGTCTTAA 0.951779 -121 AATCTGCAGAAATCGTTTTTAAAATAAAGAAAAA 6 265 1 AATGTTTTAA 0.650948 -36 atcgagttaaaaccgttttcattagcgagtccaa 7 18 1 aacgttttaa 0.930663 -283 ttggttttttagttgttttaagtatttgttattt 7 260 1 agtgttttaa 0.850527 -41 gaaagctgcaagctgtctttaataatttgcaaac 10 76 0 agcgtcttaa 0.974555 -46 gacagcttgcagctttcttttcaaccagaatttg 10 93 1 agcttcttta 0.494193 -29 cttggagcagttttttcaatcaaccgcaa 12 6 1 agcgttttta 0.935734 -164 tgtagttaaaagctgtgttaataaaacactggag 13 63 0 agcgtgttaa 0.915808 -151 aaacttactaacctggttttaataaccaacataa 14 146 1 accggtttaa 0.783698 -58 *** ***** * * Masking position 1 Map Score: 4.72133 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 104 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 AAACAAGTAATTCTAACAAATTCTAACTGC 5 19 0 TTCTAACAAA 0.955257 -74 TCGACAAAAGTTGCAACAAATTCAAAGTGA 6 221 1 TTGCAACAAA 0.94803 -80 catgagattgttcaaacaaagagcagctat 14 95 0 ttcaaacaaa 0.937107 -109 cgccaaggatttaaaacaaatatgttttat 15 103 1 ttaaaacaaa 0.845265 -44 tcgccaataattgtaacaaaattgtccaat 17 192 1 ttgtaacaaa 0.968846 -109 tgtccaataattgtaacaaaattttccgag 17 214 1 ttgtaacaaa 0.968846 -87 ********** Masking position 5 Map Score: 3.64814 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 32 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 aaatttaattgaaaaactaccacaaacttt 7 179 0 gaaaaactac 0.874384 -122 aaataatttagcaacactaccgaaatagtg 8 109 0 gcaacactac 0.942408 -79 tttattaatcgcaaaacgcctcaaggcatt 11 59 1 gcaaaacgcc 0.979596 -41 accgcaaagcgcaaaactccagcttgatta 12 33 1 gcaaaactcc 0.987928 -137 gggatgtccggcaaaacccccgaatgttcg 17 165 1 gcaaaacccc 0.979596 -136 ********** Masking position 6 Map Score: 1.66857 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 10 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: -7.01005e-13 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: -7.01005e-13 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: -7.01005e-13 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