AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i214_mgen_mpneu_300.orf -o214_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: RMP00226 30 Mycoplasma_pneumoniae Input sequences: #1 RMG03266 52 Mycoplasma #2 RMG03264 97 Mycoplasma #3 RMG03260 188 Mycoplasma #4 RMP00221 157 Mycoplasma_pneumoniae #5 RMP00223 45 Mycoplasma_pneumoniae Motif number 1 TAATATTAAAATAGAATGCGGTT 1 1 1 TATATAAATA 0.839712 -52 TGCATATATTTAGATACAAAACCGCATTCTATT 1 20 0 TAATAAAACC 0.828873 -33 TAATAATGACAAATCAACCCACTGTT 2 82 0 TATGAAAACA 0.825709 -16 CATCTAAACAAATTAACAAAGCCATTTAACTT 3 10 0 AATAAAAACC 0.955071 -179 TATAGATTTAAATATCGAAAATATCGAGAGAAT 3 43 1 AAATCAAATA 0.704673 -146 TTTTTATTTTTATTAATAAATTCTCTCGATATT 3 62 0 TATAAAAATC 0.97265 -127 TTTATTAATAAAAATAAAAACTATATTTATTAT 3 75 1 AAATAAAATA 0.837994 -114 TTATTATAAGTAATAAGTAAGTAGGAGAATTTA 3 101 1 TATAATAATA 0.849182 -88 CCAAGGTTAGAAGTAATAAATTCTCCTACTTAC 3 117 0 AATAAAAATC 0.965964 -72 CACGTTGAATTATAACAAAATTAGAAAACGGCT 3 155 0 TAAACAAATA 0.888564 -34 TAATTAATAAACACGTTGAATTA 3 176 0 TATTATAACA 0.682155 -13 aattactaataactatcaaagtcatct 4 5 0 aatataaatc 0.852871 -153 tgatagttattagtaattaattagttaacagcc 4 20 1 tataataata 0.849182 -138 ccaaacttataataaataaaccaaaacaaccac 4 61 0 aaaaaaaaca 0.910621 -97 aattataacaaaataagaaattagcccagtcaa 4 119 0 aataaaaata 0.966254 -39 gggatgaccctagtactaaaatcaataagacta 5 19 1 tatacaaatc 0.943272 -27 ** *** *** ** Masking position 9 Map Score: 16.9104 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 489 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 GTACCTTTCAAATTTTAATTGCTAATCTTT 2 18 0 AATTTTAATT 0.673756 -80 TGGGTTGATTTGTCATTATTA 2 87 1 TGTCATTATT 0.850757 -11 TAATAAATATAGTTTTTATTTTTATTAATA 3 77 0 AGTTTTTATT 0.901253 -112 AAACTATATTTATTATAAGTAATAAGTAAG 3 92 1 TATTATAAGT 0.88495 -97 CAAGGTTAGAAGTAATAAATTCTCCTACTT 3 119 0 AGTAATAAAT 0.737149 -70 TTTCTAATTTTGTTATAATTCAACGTGTTT 3 161 1 TGTTATAATT 0.960737 -28 tgactttgatagttattagtaattaattag 4 14 1 agttattagt 0.928892 -144 ttggtttatttattataagtttgggggctg 4 70 1 tattataagt 0.88495 -88 tttcttattttgttataattcaacaagtat 4 132 1 tgttataatt 0.960737 -26 taattcaacaagtattaattc 4 147 1 agtattaatt 0.864036 -11 ********** Masking position 6 Map Score: 9.73386 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 212 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 ATAATGACAAATCAACCCACTGTTCTAGATT 2 75 0 ATCACCCACT 0.997138 -23 ttaattagttaacagcccacttaaggtggtt 4 36 1 aacacccact 0.994673 -122 aataaaccaaaacaaccaccttaagtgggct 4 49 0 aacaccacct 0.959924 -109 accccacaaaatcagcccccaaacttataat 4 81 0 atcaccccca 0.986163 -77 aaaataagaaattagcccagtcaaggggtga 4 112 0 attacccagt 0.965715 -46 tagtactagggtcatcccagtaacaa 5 6 0 gtcacccagt 0.985206 -40 **** ****** Masking position 4 Map Score: 7.22493 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 15 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 4 TAATATTAAAATAGAATGCGGTTT 1 4 1 TATAAAATAG 0.530512 -49 TATCTAAATATATGCAAAAAACATCG 1 37 1 TATCAAAAAA 0.845689 -16 AGGTACATGCTAAAGAAAATATCTCTTTTTG 2 42 1 TAAGAAAATA 0.921584 -56 TGTTCTAGATTATCAAAAAGAGATATTTTCT 2 55 0 TATAAAAAGA 0.775275 -43 TCTATACATCTAAACAAATTAACAAAGCCAT 3 18 0 TAACAAATTA 0.882158 -171 TAGATTTAAATATCGAAAATATCGAGAGAAT 3 45 1 TATGAAAATA 0.845636 -144 GAGAATTTATTAATAAAAATAAAAACTATAT 3 70 1 TAAAAAAATA 0.959171 -119 TTATTACTTATAATAAATATAGTTTTTATTT 3 86 0 TAAAAATATA 0.916988 -103 CGTTGAATTATAACAAAATTAGAAAACGGCT 3 155 0 TAAAAAATTA 0.939221 -34 TAATTAATAAACACGTTGAAT 3 178 0 TAATAATAAA 0.778928 -11 agtgggctgttaactaattaattactaataa 4 26 0 taataattaa 0.693563 -132 cccaaacttataataaataaaccaaaacaac 4 64 0 taaaaataaa 0.918087 -94 tgttgaattataacaaaataagaaattagcc 4 126 0 taaaaaataa 0.939302 -32 *** ******* Masking position 6 Map Score: 12.8999 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 456 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 TAATAAATTCTCCTACTTACTTATTACTTA 3 107 0 TCCTACTTAC 0.869021 -82 ttagttaacagcccacttaaggtggttgtt 4 40 1 gcccacttaa 0.983988 -118 cacaaaatcagcccccaaacttataataaa 4 78 0 gcccccaaac 0.964457 -80 aaggggtgaaccccacaaaatcagccccca 4 91 0 ccccacaaaa 0.946253 -67 taagaaattagcccagtcaaggggtgaacc 4 109 0 gcccagtcaa 0.964282 -49 actagggtcatcccagtaacaa 5 3 0 tcccagtaac 0.969807 -43 ********** Masking position 9 Map Score: 1.4045 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 25 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 6 ********** No masking Map Score: -1.0918e-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: -1.0918e-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: -1.0918e-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