AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_mpneu_reg_100.orf -o294_mpneu_100.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMP00673 25 Mycoplasma_pneumoniae Input sequences: #1 RMP00207 76 Mycoplasma_pneumoniae #2 RMP00208 300 Mycoplasma_pneumoniae #3 RMP00212 86 Mycoplasma_pneumoniae #4 RMP00274 121 Mycoplasma_pneumoniae #5 RMP00287 27 Mycoplasma_pneumoniae #6 RMP00288 42 Mycoplasma_pneumoniae #7 RMP00296 54 Mycoplasma_pneumoniae #8 RMP00624 300 Mycoplasma_pneumoniae #9 RMP00677 300 Mycoplasma_pneumoniae Motif number 1 cttaaaggcgttggcgaaaggtaattttattaaattgcggactt 1 36 1 ttgaagataa 0.983823 -41 taaattggctttgggttaagggattttaacttaagttgcttttg 2 18 1 ttgtagttaa 0.962465 -283 taattttagcttgtgaaataggttttgctttcattccttttcca 2 104 1 ttgaagttat 0.935667 -197 ctctaactacttgtttaagcgcttttttggcaaaaactttgaag 4 17 1 ttgaagttaa 0.990384 -105 tgttttatctgtgataaatcggtttatattgccattaatt 7 7 0 gtgaagttca 0.881947 -48 acaaaccgaattgtgaaaccgtgtttttaccacaaccaatcgtt 8 214 1 ttgaagttca 0.975412 -87 gtggtttgtctcgttcaattgaattaattactaacgattggttg 8 246 0 tcgaagttaa 0.984789 -55 agcaattagattggtaaagtgtgatacgtttcaaccgcggttac 9 31 1 ttgaagataa 0.983855 -270 tgcgttttcatcgccgaatcgttttctgaaagaccattgatttg 9 74 0 tcgaagttac 0.931042 -227 agacgcagtcttgtcgaatggaaattcgcaaaaacattgtcacg 9 226 0 ttgaagataa 0.983857 -75 agactgcgtctcgatctagtgtaataacgaacaaatttcctttc 9 259 1 tcgtagataa 0.904499 -42 *** ** * ** ** Masking position 8 Map Score: 10.873 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 37 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 cacaaaatgtaacagcaacttaaaggcgttggcg 1 18 1 aacaattaaa 0.984853 -59 cccttaacccaaagccaatttacacgagt 2 6 0 aacaattaca 0.93824 -295 cgaacttaacaaaagcaacttaagttaaaatccc 2 37 0 aacaattaag 0.969496 -264 agaacttaataattacaactcgaacttaacaaaa 2 57 0 aacaatcgaa 0.881317 -244 ttcctacgttaacgacaaaataaagcgtgattat 2 188 1 aacaaataaa 0.95359 -113 actacgatggaaggtcaagtcaaaatgaggcaag 2 266 0 aacaatcaaa 0.969496 -35 ttgcaaggttaaatataatttaagta 5 12 1 aataattaag 0.757033 -16 ttggtttaagaattacaatttaaacgatattaaa 6 18 1 aacaattaaa 0.984853 -25 aattaatggcaatataaaccgatttatc 7 5 1 aacaaataaa 0.95359 -50 ** *** ***** Masking position 7 Map Score: 8.2566 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 46 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 aggtaattttattaaattgcggacttatttc 1 54 1 attaaatgcg 0.779593 -23 aagttgcttttgttaagttcgagttgtaatt 2 50 1 tgttaattcg 0.924384 -251 attatttataatttaaattcggacaatcgtt 3 44 0 atttaattcg 0.962438 -43 cttaaattatatttaaccttgcaaa 5 5 0 atttaacttg 0.632262 -23 atttaatatcgtttaaattgt 6 32 0 atttaaatcg 0.821164 -11 ataaaacaggttttaacttcgt 7 43 1 ttttaattcg 0.972431 -12 tggttttaggtgtagatttcgtttggttttt 8 105 1 tgtagattcg 0.627915 -196 gaccattgatttgtaaccgcggttgaaacgt 9 56 0 ttgtaacgcg 0.864706 -245 acgcagaacattttaatctcgtagttgatgc 9 113 1 ttttaactcg 0.970577 -188 atcgacgaaattttgacctcgcctttttgaa 9 191 1 ttttgactcg 0.919566 -110 cctcgcctttttgaaatttcgtgacaatgtt 9 207 1 ttgaaattcg 0.887063 -94 gtcttgtcgaatggaaattcgcaaaaacatt 9 232 0 atggaattcg 0.769943 -69 ****** **** Masking position 6 Map Score: 7.13949 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 113 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 tttccaagtttcacttttttgataaccattc 2 142 1 tcactttttg 0.929248 -159 tgaccttccatcgtagttttgttaagtt 2 283 1 tcgtgttttg 0.975987 -18 acttgtttaagcgcttttttggcaaaaactt 4 25 1 gcgctttttg 0.968902 -97 actaaaacaatcgttattgtggttttaggtg 8 86 1 tcgtattgtg 0.947353 -215 cccacctaaatcgcgtttgtgatggtccagc 9 143 1 tcgctttgtg 0.991888 -158 ggtcaaaatttcgtcgatgtgaatttattat 9 178 0 tcgtgatgtg 0.910632 -123 aattttgacctcgcctttttgaaatttcgtg 9 199 1 tcgctttttg 0.990221 -102 **** ****** Masking position 8 Map Score: 4.89229 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 43 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 gcaatttaataaaattacctttcgccaacg 1 44 0 aaaattacct 0.906071 -33 aaaccgtgaccaaatttcctacgttaacga 2 173 1 caaatttcct 0.97195 -128 aaaatgaggcaagatgtccttattttcatg 2 249 0 aagatgtcct 0.901968 -52 aattattcttaataattcctcgaacgtcaa 8 172 0 aataattcct 0.876116 -129 aattattaagaataattcctcctactgtta 8 185 1 aataattcct 0.876116 -116 ctacgagattaaaatgttctgcgttttcat 9 107 0 aaaatgttct 0.745689 -194 aggcgaggtcaaaatttcgtcgatgtgaat 9 185 0 aaaatttcgt 0.949059 -116 tcgcctttttgaaatttcgtgacaatgttt 9 209 1 gaaatttcgt 0.851522 -92 taataacgaacaaatttcctttccctttcg 9 280 1 caaatttcct 0.97195 -21 ********** Masking position 4 Map Score: 4.5111 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 61 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ggcaagatgtccttattttcatggaacgactaaac 2 237 0 cattttcaga 0.914476 -64 tataaataatccatgtttttagctaatgtaat 3 65 1 cgtttttaca 0.981869 -22 atgccagcttcaaagtttttgccaaaaaagcgctt 4 33 0 cgtttttgca 0.963597 -89 cagcttgcagctttcttttcaaccagaatttgcgc 4 95 1 ccttttcaca 0.924073 -27 atgtacctatcaggatttttagggaattgtgttgg 8 30 0 catttttaga 0.916029 -271 aattgtgaaaccgtgtttttaccacaaccaatcgt 8 222 1 cgtttttacc 0.978103 -79 ttaaaatgttctgcgttttcatcgccgaatcgttt 9 94 0 cgttttcacc 0.97767 -207 ttcacatcgacgaaattttgacctcgcctttttga 9 186 1 cattttgacc 0.864577 -115 aatttcgtgacaatgtttttgcgaatttccattcg 9 221 1 cgtttttgga 0.931701 -80 * ******* * * Masking position 8 Map Score: 4.04357 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 68 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 acagcaacttaaaggcgttggcgaaaggtaa 1 29 1 aaggcgttgg 0.996332 -48 actcgtgtaaattggctttgggttaagggat 2 11 1 atggctttgg 0.938749 -290 aagctaaaattacggcgctggtttcagaact 2 85 0 taggcgctgg 0.974322 -216 aagggcgttggtttaagaatt 6 1 1 aaggcgttgg 0.996332 -42 atttttagggaattgtgttggatacagattt 8 20 0 aatgtgttgg 0.866674 -281 tgcccacctaaatcgcgtttgtgatggtcca 9 141 1 aacgcgtttg 0.889843 -160 tgaatttattatgggggctggaccatcacaa 9 159 0 atggggctgg 0.948 -142 ** ******** Masking position 9 Map Score: 5.06203 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 53 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 ttattcaatagtctacataaatgtacctatc 8 54 0 gtctactaaa 0.923611 -247 ggcaatttttgtccactgaaaaaccaaacga 8 123 0 gtccacgaaa 0.985517 -178 gacaaaaattgcccaccgaaaaattaacacc 8 141 1 gcccacgaaa 0.993526 -160 cgtagttgatgcccacctaaatcgcgtttgt 9 132 1 gcccactaaa 0.993015 -169 tgatggtccagcccccataataaattcacat 9 162 1 gccccctaat 0.951138 -139 ****** **** Masking position 9 Map Score: 2.30581 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 = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ttaaattcggacaatcgttaaccgttttac 3 33 0 acaatcgtta 0.98496 -54 taaaactaaaacaatcgttattgtggtttt 8 82 1 acaatcgtta 0.98496 -219 tttaccacaaccaatcgttagtaattaatt 8 239 1 ccaatcgtta 0.990225 -62 ttttcatcgccgaatcgttttctgaaagac 9 84 0 cgaatcgttt 0.937326 -217 ********** Masking position 5 Map Score: 2.56195 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 3 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 gttcgagttgtaattattaagttctgaaac 2 66 1 taattattaa 0.93578 -235 tcaggaggaaaaagtagtaaaacggttaac 3 17 1 aaagtagtaa 0.767892 -70 gtccgaatttaaattataaataatccatgt 3 51 1 aaattataaa 0.874234 -36 ctttgtttgcaaattattaaagacagcttg 4 72 1 aaattattaa 0.949969 -50 gtttaaattgtaattcttaaaccaacgccc 6 13 0 taattcttaa 0.794795 -30 aaaaagtataaatctgtatcca 8 3 1 aaagtataaa 0.797419 -298 gacgttcgaggaattattaagaataattcc 8 174 1 gaattattaa 0.895328 -127 tcaattgaattaattactaacgattggttg 8 246 0 taattactaa 0.817291 -55 ********** Masking position 3 Map Score: 2.46355 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 54 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 11 ********** No masking Map Score: 2.56749e-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 12 ********** No masking Map Score: 2.56749e-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 13 ********** No masking Map Score: 2.56749e-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