AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i008_mgen_mpneu_300.orf -o008_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: RMG04181 117 Mycoplasma Input sequences: #1 RMG04180 264 Mycoplasma #2 RMP00121 277 Mycoplasma_pneumoniae #3 RMP00122 123 Mycoplasma_pneumoniae Motif number 1 CTAATTAACCTTTAATCTTTCAATA 1 1 0 TTAATTAATA 0.895116 -264 AGTGTGAATTTAAAAACTTCAAATAGTTGTTTATT 1 42 0 TAAATTAATA 0.966848 -223 GTTTTTAAATTCACACTTTGAAAAACTTGTGTAAC 1 60 1 TACATTAAAA 0.936878 -205 ACTAACAGTTTTAAATGTTACACAAGTTTTTCAAA 1 76 0 TAAATTACAA 0.881784 -189 AAAAGAAGGTTTAAATTTTGGTATATAACCACTTT 1 122 1 TAAATTTATA 0.845282 -143 CCACTTTTAGTCTAAAATAGCAAAAACTGCTTTTT 1 150 1 TTAATAAAAA 0.937354 -115 CACTTTTTCGTAAAAAAAAAAAAAAAAAAAGCAGT 1 175 0 TAAAAAAAAA 0.905601 -90 GAAAAAGTGGCTAAAACTAAAAATAATTATTGATA 1 201 1 CAAATAAATA 0.894352 -64 AATAAAAGATCGAAATTTATCAATAATTATTTTTA 1 218 0 CAAATAAATA 0.894352 -47 AAGCGTTTATTAAAAAAATCAAAATAAAAGATCG 1 241 0 TAAAAAAAAA 0.905587 -24 gatttggtgttcaaacctaaaaaaaggtttgctaa 2 104 0 taaataaaaa 0.980819 -174 taactaaccatttaagttttcaaaacgatcaagat 2 177 1 ttaattaaaa 0.937093 -101 taccgtcgggtaacagttagataaagctattacct 2 222 1 tacatataaa 0.735799 -56 atgtgctagttcaaagcttataaaactgaaaaggt 2 253 0 taaattaaaa 0.980818 -25 * *** ** **** Masking position 5 Map Score: 15.0809 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 372 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 2 AGAACTAACCAAAAGAAGGTTTAAATTTTG 1 112 1 AAAAGAAGGT 0.931794 -153 TATTTTAGACTAAAAGTGGTTATATACCAA 1 139 0 TAAAAGTGGT 0.931452 -126 AAAAAAAAAAAAAAAAAAGCAGTTTTTGCT 1 168 0 AAAAAAAAGC 0.806869 -97 TTTTTTTACGAAAAAGTGGCTAAAACTAAA 1 192 1 AAAAAGTGGC 0.861059 -73 TGGCTAAAACTAAAAATAATTATTGATAAA 1 208 1 TAAAAATAAT 0.705323 -57 gttcaaacctaaaaaaaggtttgctaaact 2 101 0 aaaaaaaggt 0.910556 -177 gggaacttgaaaaaggtagtggttgaaatg 2 139 1 aaaaggtagt 0.958627 -139 ttcaaaacgatcaagatagtaaactaatac 2 195 1 tcaagatagt 0.888914 -83 tataaaactgaaaaggtaatagctttatct 2 240 0 aaaaggtaat 0.781166 -38 tgatcacggttaaagatagtcttaataagg 3 27 0 taaagatagt 0.954233 -97 ttaaccgtgatcaaaaaagtgcaccacgct 3 44 1 tcaaaaaagt 0.778552 -80 ********** Masking position 4 Map Score: 8.72691 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 469 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 TTGAAAGATTAAAGGTTAATTAGATACAGAAT 1 13 1 AAGTTAATTA 0.958938 -252 TAACATTTAAAACTGTTAGTAAGAACTAACCA 1 91 1 AAGTTAGTAA 0.914578 -174 AAGCGTTTATTAAAAAAATCAA 1 253 0 AAGTTTATTA 0.958937 -12 ttaatgccataaacgattgctatttattg 2 8 0 aagattgcta 0.928185 -270 aaacctaaaaaaaggtttgctaaacttaggtg 2 95 0 aagtttgcta 0.986329 -183 tgaaaacttaaatggttagttaactaggttca 2 167 0 aagttagtta 0.983537 -111 acccgacggtattagtttactatcttgatcgt 2 201 0 atgtttacta 0.834816 -77 accgtcgggtaacagttagataaagctattac 2 223 1 aagttagata 0.947805 -55 ** ******** Masking position 1 Map Score: 7.27699 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 81 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 AAAGTGTGAATTTAAAAACTTCAAATAGTTG 1 48 0 TTTAAAAATT 0.611745 -217 AATTCACACTTTGAAAAACTTGTGTAACATT 1 67 1 TTGAAAAATT 0.956445 -198 TTAAAACTGTTAGTAAGAACTAACCAAAAGA 1 97 1 TAGTAAGACT 0.596548 -168 TAGTCTAAAATAGCAAAAACTGCTTTTTTTT 1 157 1 TAGCAAAACT 0.957016 -108 TACGAAAAAGTGGCTAAAACTAAAAATAATT 1 198 1 TGGCTAAACT 0.916598 -67 AAAATAATTATTGATAAATTTCGATCTTTTA 1 220 1 TTGATAAATT 0.948663 -45 ttaggtgagattgcaagatctcgtttaaatt 2 71 0 ttgcaagact 0.950913 -207 aaaaaaaggtttgctaaacttaggtgagatt 2 90 0 ttgctaaatt 0.945301 -188 aatcgggaacttgaaaaaggtagtggttgaa 2 135 1 ttgaaaaagt 0.908192 -143 gggtaacagttagataaagctattacctttt 2 229 1 tagataaact 0.952458 -49 cgaaaacgaattgacaaagctacgtgataaa 3 79 1 ttgacaaact 0.94843 -45 acaaagctacgtgataaatcttcttcctcct 3 92 1 gtgataaact 0.896206 -32 ******** ** Masking position 6 Map Score: 11.6708 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 316 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 GAAAGATTAAAGGTTAATTAGATACAGAAT 1 15 1 AGGTTAATTA 0.939844 -250 AACCTTCTTTTGGTTAGTTCTTACTAACAG 1 103 0 TGGTTAGTTC 0.940703 -162 AGACTAAAAGTGGTTATATACCAAAATTTA 1 133 0 TGGTTATATA 0.902137 -132 tgctaaacttaggtgagattgcaagatctc 2 80 0 aggtgagatt 0.892725 -198 ttagttaactaggttcatttcaaccactac 2 154 0 aggttcattt 0.827855 -124 aaaacttaaatggttagttaactaggttca 2 167 0 tggttagtta 0.964343 -111 agtcttaataaggttatattaaagattga 3 10 0 aggttatatt 0.923097 -114 ********** Masking position 4 Map Score: 2.45754 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 129 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ********** No masking Map Score: 1.58694e-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 7 ********** No masking Map Score: 1.58694e-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 8 ********** No masking Map Score: 1.58694e-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