AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_mgen_mpneu_100.orf -o030_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 RMG01136 197 Mycoplasma #2 RMG05235 158 Mycoplasma #3 RMP00104 182 Mycoplasma_pneumoniae #4 RMP00112 300 Mycoplasma_pneumoniae Motif number 1 ATCTTAGCAATAATATTTATTTAAACGTTAATGA 1 19 0 TAAATTTTAA 0.807675 -179 TTAATTTAGCTAAAAAATGATTAAAGTTTGCTAA 1 66 0 TAAAATTTAA 0.962972 -132 TAGCTAAATTAAACAACCAGTTAATTAGTAAACA 1 88 1 AAAAACTTAA 0.966377 -110 AAATACAAAATAAAAACTAACTAATATTTGATTT 1 134 0 TAAAATCTAA 0.955293 -64 TTTTTACTAAAAATAATTAGCTAAAATACCGTCA 2 14 0 AAAAATCTAA 0.969259 -145 AAGTAGTATCAAACATTTTTTTATCTTTTGATTT 2 49 0 AAAATTTTAT 0.684498 -110 CTTTTTTGCAAAATAACTAACTAAATACTAGAAG 2 127 1 AAAAATCTAA 0.969259 -32 atcaacgatctaataagttactattacgcatatt 3 32 0 taaaatctat 0.882004 -151 agtggttttttaaaaaacatttaactcttattta 3 78 0 taaaacttaa 0.944765 -105 tttctgtaactattaattagttaagccttt 3 163 1 tataatttaa 0.690045 -20 cgaagatccgaaaaaagtaaataatgtcgaaaaa 4 19 1 aaaaatataa 0.829837 -282 taatgtcgaaaaagaaccgactatttaaatgttt 4 40 1 aaaaacctat 0.892069 -261 ccgtttacgtcaacaaacatttaaatagtcggtt 4 54 0 caaaacttaa 0.857017 -247 ttagttcccgaaataaacttttaactgggcaatt 4 106 1 aaaaacttaa 0.964565 -195 aaaagtcaaaataaaactttttaagatttattct 4 208 1 ataaatttaa 0.751003 -93 tgactatcgaaaagaattttttattgaaaaactc 4 253 1 aaaaatttat 0.930294 -48 *** ** * **** Masking position 5 Map Score: 22.3772 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 286 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 GTTAGCAAACTTTAATCATTTTTTAGCTAAATTAAAC 1 65 1 TTTACTTTGC 0.835628 -133 TTATTTTGTATTTTCAAAATTCTACTCAATTAGGATG 1 155 1 TTTTATTTTC 0.940212 -43 TATGACGGTATTTTAGCTAATTATTTTTAGTAAAAAG 2 12 1 TTTTCATATT 0.693388 -147 TCAAACATTTTTTTATCTTTTGATTTCTTTTTACTAA 2 38 0 TTTTCTTATC 0.992934 -121 acgccgatgcttttatcgtttaaagttttgcagagct 3 117 0 ttttcttatt 0.951278 -66 agtcggttctttttcgacattatttacttttttcgga 4 25 0 ttttatttac 0.813831 -276 cgtgaaaacattttacccgtttacgtcaacaaacatt 4 67 0 ttttcttatc 0.992934 -234 gggtaaaatgttttcacgatttagttcccgaaataaa 4 86 1 ttttcttatc 0.992934 -215 taactgggcaatttttcaattaattaccctcctattc 4 127 1 atttcttaac 0.818986 -174 cgttcgaaatttttcgcgttttatcgcaaattttttg 4 163 1 ttttcttagc 0.983719 -138 aaaagttttattttgacttttgtcatccacaaaaaat 4 192 0 ttttcttttc 0.990298 -109 aaataaaactttttaagatttattctctatattaaaa 4 216 1 ttttgttttc 0.929665 -85 **** * ** * ** Masking position 11 Map Score: 13.932 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 88 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 AATAATATTTATTTAAACGTTAATGATATA 1 15 0 ATTTAAACGT 0.760297 -183 TTTGCTAACAAGTTTAAAGTAATCTTAGCA 1 44 0 AGTTTAAAGT 0.892326 -154 CCAGTTAATTAGTAAACAGTTCCAGAATTA 1 104 1 AGTAAACAGT 0.883601 -94 AATTATTTTTAGTAAAAAGAAATCAAAAGA 2 30 1 AGTAAAAAGA 0.939216 -129 tttaaataagagttaaatgttttttaaaaa 3 76 1 agttaaatgt 0.967915 -107 atgcttttatcgtttaaagttttgcagagc 3 118 0 cgtttaaagt 0.825835 -65 ctcgaagatccgaaaaaagtaaataatgtc 4 17 1 cgaaaaaagt 0.846048 -284 agaaccgactatttaaatgtttgttgacgt 4 52 1 atttaaatgt 0.896626 -249 gacgtaaacgggtaaaatgttttcacgatt 4 77 1 ggtaaaatgt 0.879389 -224 aaaattgcccagttaaaagtttatttcggg 4 112 0 agttaaaagt 0.976438 -189 gagaataaatcttaaaaagttttattttga 4 213 0 cttaaaaagt 0.885507 -88 tattctctatattaaaatgactatcgaaaa 4 236 1 attaaaatga 0.763389 -65 cccgcttttaagaaaaatgatta 4 288 1 agaaaaatga 0.696278 -13 ********** Masking position 6 Map Score: 12.5834 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 184 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 ATAAATATTATTGCTAAGATTACTTTAAAC 1 33 1 TTGCTAAGAT 0.839517 -165 TGATTAAAGTTTGCTAACAAGTTTAAAGTA 1 53 0 TTGCTAACAA 0.923639 -145 TTGTTTAATTTAGCTAAAAAATGATTAAAG 1 74 0 TAGCTAAAAA 0.972548 -124 CTGGAACTGTTTACTAATTAACTGGTTGTT 1 99 0 TTACTAATTA 0.843704 -99 AAATAAAAACTAACTAATATTTGATTTTAA 1 131 0 TAACTAATAT 0.824694 -67 TAAAAATAATTAGCTAAAATACCGTCATAT 2 11 0 TAGCTAAAAT 0.934662 -148 TGATTTCTTTTTACTAAAAATAATTAGCTA 2 25 0 TTACTAAAAA 0.962436 -134 GTTAGTTATTTTGCAAAAAAGGATTAGTTT 2 118 0 TTGCAAAAAA 0.844299 -41 GCAAAATAACTAACTAAATACTAGAAGATT 2 134 1 TAACTAAATA 0.899231 -25 aattacaccctttctaaaaaatatgcgtaa 3 13 1 tttctaaaaa 0.865826 -170 aaaggcttaactaattaatagttacag 3 166 0 taactaatta 0.822955 -17 ********** Masking position 6 Map Score: 10.031 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 258 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 ACTTTAATCATTTTTTAGCTAAATTAAACA 1 73 1 TTTTTTAGCT 0.805301 -125 TTGATTTTAATTCTGGAACTGTTTACTAAT 1 111 0 TTCTGGAACT 0.96734 -87 TTAGTTTTTATTTTGTATTTTCAAAATTCT 1 148 1 TTTTGTATTT 0.817608 -50 TATCAAACATTTTTTTATCTTTTGATTTCT 2 47 0 TTTTTTATCT 0.901784 -112 TGATTTACTTTTTGGTATCTCTATAAAAAG 2 80 0 TTTGGTATCT 0.964301 -79 gtcaaggcatttctgtaactattaattagt 3 154 1 ttctgtaact 0.967967 -29 tatttacttttttcggatcttcgagaataa 4 12 0 tttcggatct 0.93501 -289 aaaagtttatttcgggaactaaatcgtgaa 4 98 0 ttcgggaact 0.952223 -203 ********** Masking position 7 Map Score: 4.6468 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 74 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 AAAAATGATTAAAGTTTGCTAACAAGTTTA 1 58 0 AAAGTTTGCT 0.84835 -140 TAATTTAGCTAAAAAATGATTAAAGTTTGC 1 69 0 AAAAAATGAT 0.813562 -129 TCAAAAGATAAAAAAATGTTTGATACTACT 2 52 1 AAAAAATGTT 0.79622 -107 ccctttctaaaaaatatgcgtaatagtaac 3 20 1 aaaatatgcg 0.962151 -163 taattaattgaaaaattgcccagttaaaag 4 123 0 aaaaattgcc 0.938322 -178 ataaaacgcgaaaaatttcgaacgaatagg 4 157 0 aaaaatttcg 0.901991 -144 tcatccacaaaaaatttgcgataaaacgcg 4 177 0 aaaatttgcg 0.962132 -124 gtttttcaataaaaaattcttttcgatagt 4 255 0 aaaaaattct 0.865792 -46 ********** Masking position 3 Map Score: 4.08887 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 190 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: 1.11088e-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: 1.11088e-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: 1.11088e-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