AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_mgen_mpneu_100.orf -o222_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 RMG01441 300 Mycoplasma #2 RMG02475 58 Mycoplasma #3 RMP00040 89 Mycoplasma_pneumoniae #4 RMP00042 300 Mycoplasma_pneumoniae #5 RMP00050 300 Mycoplasma_pneumoniae Motif number 1 CACATTCATTAATAAAAGATACGCTTTCAA 1 33 0 AATAAAAGAT 0.876972 -268 GCTGTGTTTAAATAATAGTTGCTTAGTTCC 1 62 0 AATAATAGTT 0.964849 -239 TGGGAACAGAAATAAAAGATTAACATGACT 1 126 1 AATAAAAGAT 0.876972 -175 TAAATTGCACAAAAAAAGCTTTTTGACAAA 1 181 1 AAAAAAAGCT 0.874069 -120 TTTTTGACAAAAAAATAGTTATTTTTTGTA 1 200 1 AAAAATAGTT 0.969401 -101 ATTAAGTAACAATAATAGTTTAGTTTGTTA 1 244 0 AATAATAGTT 0.964849 -57 TTATTACTATCAAGATAGTTACCAACTATT 2 17 1 CAAGATAGTT 0.88066 -42 GTTTTACTAACAAAATAGTTGGTAACTATC 2 30 0 CAAAATAGTT 0.958949 -29 attgtgattccaaaaaacttgcttccatac 4 214 1 caaaaaactt 0.759648 -87 ctcgtccgagcaaaaaagttgtgttcagtg 5 144 1 caaaaaagtt 0.964367 -157 cgaaaaccgaaaaaatattttgggacagtt 5 197 0 aaaaatattt 0.81304 -104 tttatttatcaatgaaattttcgaaaaccg 5 218 0 aatgaaattt 0.582695 -83 ttcattgataaataaacgtttaatcacgtt 5 232 1 aataaacgtt 0.833827 -69 ********** Masking position 5 Map Score: 13.4863 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 362 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 AATCGCTTTTAATAAAAAATTACACGCTTTTG 1 91 0 AATAAAAATA 0.858373 -210 TAAATTAAGCAATTACAAAAAATAACTATTTT 1 211 0 AATACAAAAA 0.971291 -90 TGCTTAATTTAATAACAAACTAAACTATTATT 1 232 1 AATACAAATA 0.981908 -69 CTATCAAGATAGTTACCAACTATTTTGTTAGT 2 23 1 AGTACCAATA 0.967871 -36 ttaatgaggaattaccaattaactcaatttt 3 10 1 aataccaata 0.968488 -80 gaagaaacggaatgacaaaatacggtaaacaa 4 22 1 aatacaaata 0.981908 -279 accaaatgacagtgacaaacaaaatggtcctt 4 64 1 agtacaaaaa 0.970727 -237 gaacatcttgagtttcaaagaaaccatagtca 4 245 0 agttcaaaaa 0.855964 -56 *** ***** ** Masking position 8 Map Score: 8.68186 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 51 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 AGATACGCTTTCAAATAAATTAGGTTGGTC 1 17 0 TCAAATAAAT 0.725435 -284 AAAGCGTATCTTTTATTAATGAATGTGGAA 1 36 1 TTTTATTAAT 0.715957 -265 TTGTATAAAGTCATGTTAATCTTTTATTTC 1 134 0 TCATGTTAAT 0.880207 -167 GGAACAGAAGTTGTATAAAGTCATGTTAAT 1 144 0 TTGTATAAAG 0.792293 -157 TAGTTTGTTATTAAATTAAGCAATTACAAA 1 224 0 TTAAATTAAG 0.796879 -77 GAAGTTATATTAATTGTGCTATAT 1 287 0 TTATATTAAT 0.924022 -14 TTGTATTAAGTTTTACTAAC 2 49 0 TTGTATTAAG 0.891769 -10 gttggcaaaattgagttaattggtaattcc 3 18 0 ttgagttaat 0.895623 -72 aatttagccttcgtcttaatcttcggaaat 4 177 1 tcgtcttaat 0.736876 -124 cttctagtctttctgttaattggtttgcga 4 275 0 ttctgttaat 0.754841 -26 cttaaatgatttaaataaatttagtcgccc 5 115 1 ttaaataaat 0.78249 -186 tttgggacagttaaataaatcaccctcgtc 5 179 0 ttaaataaat 0.78249 -122 ttaattgatatcgtgttaattattgtcaac 5 280 1 tcgtgttaat 0.907924 -21 ********** Masking position 8 Map Score: 8.1544 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 149 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 ATCTTTTATTTCTGTTCCCACTAAATCGCT 1 116 0 TCTGTTCCCA 0.921966 -185 TTATACAACTTCTGTTCCCATCTACTAAAT 1 156 1 TCTGTTCCCA 0.921966 -145 aattgggacacctggtccgaatagtgtaga 4 147 1 cctggtccga 0.995275 -154 agtggagacccatctaccgaaaaaat 5 7 0 catctaccga 0.884071 -294 ttttataaaacctcgacagacggaaagtgg 5 32 0 cctcgacaga 0.940042 -269 atttagtcgccctcgtccgagcaaaaaagt 5 133 1 cctcgtccga 0.996429 -168 aataaatcaccctcgtccgtctcactgaac 5 166 0 cctcgtccgt 0.983036 -135 ********** Masking position 3 Map Score: 6.56093 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 1 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 CTAAATCGCTTTTAATAAAAAATTACACGC 1 96 0 TTTAATAAAA 0.736788 -205 AAAAAAGCTTTTTGACAAAAAAATAGTTAT 1 192 1 TTTGACAAAA 0.849907 -109 AATTGCTTAATTTAATAACAAACTAAACTA 1 229 1 TTTAATAACA 0.913173 -72 TGTATTAAGTTTTACTAACAAAATAGTTGG 2 38 0 TTTACTAACA 0.931912 -21 ttaactcaattttgccaacctctaacaatt 3 29 1 tttgccaacc 0.883068 -61 cctctaacaattttataaccgcgatatgtt 3 47 1 ttttataacc 0.841844 -43 tgttaattggtttgcgaacatcttgagttt 4 262 0 tttgcgaaca 0.934064 -39 tctgtcgaggttttataaaaactgctaacc 5 42 1 ttttataaaa 0.4891 -259 attttttcggttttcgaaaatttcattgat 5 211 1 ttttcgaaaa 0.486117 -90 ********** Masking position 7 Map Score: 4.19541 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 217 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TTTATTAAAAGCGATTTAGTGGGAACAGAA 1 107 1 GCGATTTAGT 0.978326 -194 CTTTTTTTGTGCAATTTAGTAGATGGGAAC 1 169 0 GCAATTTAGT 0.976644 -132 gaatagtgtagaaatttagccttcgtctta 4 165 1 gaaatttagc 0.945827 -136 tatcaaaacggagatgtagtttgattgtcg 5 85 0 gagatgtagt 0.949629 -216 atgatttaaataaatttagtcgccctcgtc 5 120 1 taaatttagt 0.881362 -181 ********** Masking position 5 Map Score: 1.55507 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ATATACGACCAACCTAATTTATTTGAA 1 6 1 CGACCAACAA 0.986754 -295 aatacacaatcgaccaaatgacagtgacaaac 4 52 1 cgaccaaaac 0.952197 -249 caaatgacagtgacaaacaaaatggtcctttc 4 66 1 tgacaaacaa 0.764804 -235 ggagacccatctaccgaaaaaat 5 2 0 ctaccgaaaa 0.782588 -299 tataaaacctcgacagacggaaagtggagacc 5 27 0 cgacagacaa 0.978808 -274 tgattgttttcgacaatcaaactacatctccg 5 75 1 cgacaatcac 0.912656 -226 tagtcgccctcgtccgagcaaaaaagttgtgt 5 136 1 cgtccgagaa 0.908411 -165 aaatcaccctcgtccgtctcactgaacacaac 5 161 0 cgtccgtcac 0.939475 -140 ******** ** Masking position 11 Map Score: 0.757474 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 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 8 ********** No masking Map Score: -1.09891e-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: -1.09891e-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: -1.09891e-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