AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i312_mgen_mpneu_100.orf -o312_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 RMG05344 25 Mycoplasma #2 RMG04236 300 Mycoplasma #3 RMP00155 300 Mycoplasma_pneumoniae #4 RMP00158 67 Mycoplasma_pneumoniae #5 RMP00161 22 Mycoplasma_pneumoniae Motif number 1 TTAAAAGAATCAGTATTATTAAAAGAAACT 2 154 0 CAGTATTATT 0.862226 -147 TTAATGGTAGTGATATTAGTGATTCCATTA 2 180 1 TGATATTAGT 0.774285 -121 TTTGAGGGTCTGATATTATGTGTCTATTTG 2 210 0 TGATATTATG 0.947064 -91 agtatttatttagtattatgcta 3 4 0 tagtattatg 0.973964 -297 ttaatattattagtatttatttagtattat 3 15 0 tagtatttat 0.923328 -286 taaatactaataatattaagctattagtag 3 26 1 taatattaag 0.95444 -275 agtaggtaaataatattaagataatattat 3 51 1 taatattaag 0.95444 -250 aatattaagataatattatgttaaagaaaa 3 62 1 taatattatg 0.934185 -239 tatagaagattagtatttaatagtaaacgg 3 107 1 tagtatttaa 0.791903 -194 aaaaagaaagtggtatataggaaaatggaa 3 151 0 tggtatatag 0.675707 -150 gctaccaacgtggtattaaaatgtgcccaa 3 186 0 tggtattaaa 0.931953 -115 aataccatcagggtattaagatgctaccaa 3 208 0 gggtattaag 0.91028 -93 aataccctgatggtattaatttcgtcggta 3 221 1 tggtattaat 0.977447 -80 agtattattccggtattatttaccgacgaa 3 241 0 cggtattatt 0.88746 -60 aatatttatttagtattattccggtattat 3 252 0 tagtattatt 0.958868 -49 gcttaaattctaatatttatttagtattat 3 263 0 taatatttat 0.820483 -38 ********** Masking position 5 Map Score: 23.0955 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 129 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 AAAGGCGATGTTAATGAAAAAGATAAACTCT 2 44 1 TTAATGAAAA 0.727926 -257 TTTTCTTGCTAAAAAGAGTTTATCTTTTTCA 2 58 0 AAAAAGAGTT 0.793753 -243 AGAGGTATTTTAAAAGCATATGGAGAAGCCA 2 89 1 TAAAAGCATT 0.89473 -212 ATATTGCTGAAAAAAGAATTTATAAAGGGTT 2 120 1 AAAAAGAATT 0.948596 -181 TCAGTATTATTAAAAGAAACTGCTAACCCTT 2 144 0 TAAAAGAAAT 0.976051 -157 TCACTACCATTAAAAGAATCAGTATTATTAA 2 162 0 TAAAAGAATA 0.965323 -139 GATGGTTTAATTAAAGAAACTATCTCA 2 284 1 TTAAAGAAAT 0.965323 -17 taatattatgttaaagaaaaagtttctctat 3 72 1 ttaaagaaaa 0.950036 -229 cccaaccgcgaaaaagaaagtggtatatagg 3 160 0 aaaaagaaat 0.948597 -141 aattaaacacttaaagaattataaaagga 4 9 0 ttaaagaata 0.950033 -59 ********* * Masking position 4 Map Score: 11.4541 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 235 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 AAGAAAAAGAGGTATTTTAAAAGCATATGG 2 82 1 GGTATTTTAA 0.935858 -219 TAAAAGAATCAGTATTATTAAAAGAAACTG 2 153 0 AGTATTATTA 0.881057 -148 GGTTACCACTAGCATCATAAATAAGGTTTT 2 237 0 AGCATCATAA 0.964618 -64 ttaacataatattatcttaatattatttac 3 56 0 attatcttaa 0.738235 -245 ctaccaacgtggtattaaaatgtgcccaac 3 185 0 ggtattaaaa 0.807492 -116 ccacgttggtagcatcttaataccctgatg 3 203 1 agcatcttaa 0.944427 -98 aaacacttaaagaattataaaagga 4 6 0 agaattataa 0.910693 -62 tacagcgctaagtattataa 5 1 0 agtattataa 0.976379 -22 ********** Masking position 4 Map Score: 5.33482 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 40 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 AGTGGTGATAACCAAAACAAAACCATTCCC 2 11 1 ACCAAAACAA 0.892912 -290 TTAAACCATCAGCAAAATAACCTAGAAGGT 2 264 0 AGCAAAATAA 0.942407 -37 agctattagtaggtaaataatattaagata 3 44 1 aggtaaataa 0.954094 -257 taatagtaaacggcaaacaaatttgttttc 3 124 1 cggcaaacaa 0.945914 -177 tataggaaaatggaaaacaaatttgtttgc 3 136 0 tggaaaacaa 0.93435 -165 ttatttaccgacgaaattaataccatcagg 3 226 0 acgaaattaa 0.772578 -75 ttaatttcgtcggtaaataataccggaata 3 236 1 cggtaaataa 0.945147 -65 ********** Masking position 5 Map Score: 1.92685 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 118 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 attattagtatttatttagtattatgcta 3 10 0 tttatttagt 0.981899 -291 atactaatcttctatatagtatagagaaac 3 93 0 tctatatagt 0.873477 -208 cctgatggtattaatttcgtcggtaaataa 3 226 1 ttaatttcgt 0.927241 -75 aattctaatatttatttagtattattccgg 3 258 0 tttatttagt 0.981899 -43 ********** Masking position 5 Map Score: 0.698534 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 21 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 6 ********** No masking Map Score: -3.95472e-13 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: -3.95472e-13 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: -3.95472e-13 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