AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_mgen_mpneu_100.orf -o201_mgen_mpneu_100.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 RMG02253 110 Mycoplasma #2 RMG03264 97 Mycoplasma #3 RMG03260 188 Mycoplasma #4 RMP00221 157 Mycoplasma_pneumoniae #5 RMP00223 45 Mycoplasma_pneumoniae #6 RMP00624 300 Mycoplasma_pneumoniae Motif number 1 AAACAAGCTAAAAACCACAAAACCAAGGTT 1 44 0 AAAACCACAA 0.921674 -67 ATTATGCAGTAAAACTGCAATAATATTGTT 1 76 0 AAAACTGCAA 0.921036 -35 TGCATAATGTAAAATTACACAGC 1 98 1 AAAATTACAC 0.901523 -13 TTAGCAATTAAAATTTGAAAGGTACATGCT 2 23 1 AAATTTGAAA 0.59363 -75 TAATAATGACAAATCAACCCACTGTTCTAG 2 78 0 AAATCAACCC 0.954052 -20 ACATCTAAACAAATTAACAAAGCCATTTAA 3 14 0 AAATTAACAA 0.922066 -175 TTCGATATTTAAATCTATACATCTAAACAA 3 32 0 AAATCTATAC 0.740737 -157 TTTATTAATAAAAATAAAAACTATATTTAT 3 75 1 AAAATAAAAA 0.706146 -114 AATTATAACAAAATTAGAAAACGGCTCATT 3 151 0 AAATTAGAAA 0.673237 -38 taaataaaccaaaacaaccaccttaagtgg 4 52 0 aaaacaacca 0.928018 -106 gaaccccacaaaatcagcccccaaacttat 4 84 0 aaatcagccc 0.93612 -74 acaaaataagaaattagcccagtcaagggg 4 115 0 aaattagccc 0.859607 -43 attttgttataattcaacaagtattaattc 4 138 1 aattcaacaa 0.657655 -20 cctagtactaaaatcaataagactaaggg 5 27 1 aaatcaataa 0.752446 -19 actattgaataaaactaaaacaatcgttat 6 73 1 aaaactaaaa 0.803067 -228 atctacacctaaaaccacaataacgattgt 6 92 0 aaaaccacaa 0.921674 -209 aaaccaaacgaaatctacacctaaaaccac 6 104 0 aaatctacac 0.963791 -197 tgtccactgaaaaaccaaacgaaatctaca 6 115 0 aaaaccaaac 0.793782 -186 tcagtggacaaaaattgcccaccgaaaaat 6 135 1 aaaattgccc 0.781352 -166 gcccaccgaaaaattaacaccttgacgttc 6 151 1 aaattaacac 0.940067 -150 ********** Masking position 2 Map Score: 23.8721 Number of sites scoring better than the average of aligned sites = 804 Number in coding regions = 736 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 TTTATGGCTTTTAGTTATTATCGAGTTTTA 1 15 0 TTAGTTATTA 0.942775 -96 ACCTTAAAGATTAGCAATTAAAATTTGAAA 2 13 1 TTAGCAATTA 0.889252 -85 TCGAGAGAATTTATTAATAAAAATAAAAAC 3 66 1 TTATTAATAA 0.489448 -123 AATAAAAACTATATTTATTATAAGTAATAA 3 87 1 ATATTTATTA 0.696383 -102 TCCTACTTACTTATTACTTATAATAAATAT 3 97 0 TTATTACTTA 0.844215 -92 GTAGGAGAATTTATTACTTCTAACCTTGGC 3 121 1 TTATTACTTC 0.885307 -68 TTCAACGTGTTTATTAATTA 3 179 1 TTATTAATTA 0.868858 -10 ttgatagttattagtaattaattagttaac 4 19 1 ttagtaatta 0.933821 -139 ttgttttggtttatttattataagtttggg 4 65 1 ttatttatta 0.943716 -93 aattcaacaagtattaattc 4 148 1 gtattaattc 0.829756 -10 ggaattattcttaataattcctcgaacgtc 6 174 0 ttaataattc 0.835068 -127 caaccaatcgttagtaattaattcaattga 6 246 1 ttagtaatta 0.933821 -55 ********** Masking position 3 Map Score: 15.7551 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 90 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 ATCTAGAACAGTGGGTTGATTTGTCATTAT 2 76 1 GTGGGTTGAT 0.984336 -22 accaccttaagtgggctgttaactaattaa 4 36 0 gtgggctgtt 0.994652 -122 gcccacttaaggtggttgttttggtttatt 4 50 1 ggtggttgtt 0.889623 -108 ttataagtttgggggctgattttgtggggt 4 82 1 gggggctgat 0.993556 -76 caccccttgactgggctaatttcttatttt 4 113 1 ctgggctaat 0.935099 -45 taatttttcggtgggcaatttttgtccact 6 137 0 gtgggcaatt 0.939407 -164 ********** Masking position 10 Map Score: 5.44727 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 10 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 AATCTAGAACAGTGGGTTGATTTGTCATTA 2 75 1 AGTGGGTTGA 0.980141 -23 GTAATAAGTAAGTAGGAGAATTTATTACTT 3 110 1 AGTAGGAGAA 0.861972 -79 aaccaccttaagtgggctgttaactaatta 4 37 0 agtgggctgt 0.976024 -121 attataagtttgggggctgattttgtgggg 4 81 1 tgggggctga 0.926071 -77 tcaccccttgactgggctaatttcttattt 4 112 1 actgggctaa 0.957577 -46 ttgttactgggatgaccctagtact 5 6 1 actgggatga 0.981351 -40 ggtttgtaacagtaggaggaattattctta 6 191 0 agtaggagga 0.958146 -110 ********** Masking position 5 Map Score: 3.87024 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 22 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 TCAATAAAACTCGATAATAACTAAAAGCCAT 1 10 1 CTCGAAATAC 0.835427 -101 AATAACTAAAAGCCATAAAACCTTGGTTTTGT 1 26 1 AGCCAAAAAC 0.942606 -85 ACAAGCTAAAAACCACAAAACCAAGGTTTTAT 1 40 0 AACCAAAAAC 0.984085 -71 GGTACATGCTAAAGAAAATATCTCTTTTTGAT 2 43 1 AAAGAAATAC 0.912032 -55 CTATACATCTAAACAAATTAACAAAGCCATTT 3 16 0 AAACAATTAC 0.683062 -173 AGATTTAAATATCGAAAATATCGAGAGAATTT 3 46 1 ATCGAAATAC 0.929709 -143 ATTTATTAATAAAAATAAAAACTATATTTATT 3 74 1 AAAAAAAAAC 0.665185 -115 ataataaataaaccaaaacaaccaccttaagt 4 54 0 aaccaaacac 0.957644 -104 aaggggtgaaccccacaaaatcagcccccaaa 4 89 0 ccccaaaaac 0.863076 -69 ctacacctaaaaccacaataacgattgtttta 6 88 0 aaccaaatac 0.984085 -213 aattcaattgaacgagacaaaccacgtattac 6 265 1 aacgaacaac 0.897213 -36 ***** **** * Masking position 7 Map Score: 7.36205 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 145 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TTTTAGCTTGTTTATAACAATATTATTGCA 1 61 1 TTTATAACAA 0.955731 -50 TTACTTATTACTTATAATAAATATAGTTTT 3 91 0 CTTATAATAA 0.96334 -98 AACACGTTGAATTATAACAAAATTAGAAAA 3 160 0 ATTATAACAA 0.974535 -29 agcccccaaacttataataaataaaccaaa 4 69 0 cttataataa 0.96334 -89 tacttgttgaattataacaaaataagaaat 4 131 0 attataacaa 0.974535 -27 ********** Masking position 5 Map Score: 5.7254 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 AAAAGCCATAAAACCTTGGTTTTGTGGTTT 1 33 1 AAACCTTGGT 0.956401 -78 TTATTACTTCTAACCTTGGCAATGAGCCGT 3 131 1 TAACCTTGGC 0.971826 -58 tgtggggttcaccccttgactgggctaatt 4 104 1 accccttgac 0.980813 -54 cgaaaaattaacaccttgacgttcgaggaa 6 157 1 acaccttgac 0.988656 -144 ********** Masking position 6 Map Score: 0.44184 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 6 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: -1.12023e-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 9 ********** No masking Map Score: -1.12023e-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 10 ********** No masking Map Score: -1.12023e-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