AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_mgen_mpneu_300.orf -o210_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: RMP00323 42 Mycoplasma_pneumoniae Input sequences: #1 RMG01352 300 Mycoplasma #2 RMG00273 137 Mycoplasma #3 RMG02389 24 Mycoplasma #4 RMG04418 88 Mycoplasma #5 RMG03260 188 Mycoplasma #6 RMP00221 157 Mycoplasma_pneumoniae #7 RMP00677 300 Mycoplasma_pneumoniae Motif number 1 TTAAATAAAAAAAGACCATAGGT 1 288 0 AAATAAAAAA 0.706842 -13 GATTCACTACTAATAATTTAAATTAAGCACT 2 48 1 TAATAATTTA 0.795284 -90 GCACTCATACTAATATATTAATCCCTTTAGA 2 74 1 TAATATATTA 0.795182 -64 AGATAAATATTAATAAAATTACTCTGATTTA 4 23 1 TAATAAAATA 0.921316 -66 CTATACATCTAAACAAATTAACAAAGCCATT 5 17 0 AAACAAATTA 0.83093 -172 GAGAATTTATTAATAAAAATAAAAACTATAT 5 70 1 TAATAAAAAA 0.926971 -119 TTATTACTTATAATAAATATAGTTTTTATTT 5 86 0 TAATAAATAA 0.957472 -103 AGGTTAGAAGTAATAAATTCTCCTACTTACT 5 116 0 TAATAAATTT 0.795393 -73 CGTTGAATTATAACAAAATTAGAAAACGGCT 5 155 0 TAACAAAATA 0.935027 -34 TAATTAATAAACACGTTGAAT 5 178 0 TAATTAATAA 0.808697 -11 agtgggctgttaactaattaattactaataa 6 26 0 taactaatta 0.830917 -132 cccaaacttataataaataaaccaaaacaac 6 64 0 taataaataa 0.957497 -94 tgttgaattataacaaaataagaaattagcc 6 126 0 taacaaaata 0.937208 -32 ccagcccccataataaattcacatcgacgaa 7 169 1 taataaatta 0.975282 -132 ********* * Masking position 3 Map Score: 16.0981 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 171 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 CAAAAACGACAATCTTTTAGTTGATAAATACCTTT 1 118 0 AATTTGTGAT 0.96799 -183 ACTCTTTAAAACTTCCCTTTATAATCAAATATCGC 2 112 1 ACTCTTTAAT 0.490154 -26 AAATCAGAGTAATTTTATTAATATTTATCTAACTT 4 18 0 AATTTATATT 0.687289 -71 AGGCATTAACAATGTCTTTTTTAAGTCCATTAAAT 4 49 0 AATTTTTAAG 0.735032 -40 AAGTTAAATGGCTTTGTTAATTTGTTTAGAT 5 7 1 AATGTGTAAT 0.920137 -182 TTTATTAATAAATTCTCTCGATATTTTCGATATTT 5 52 0 AATCTGTATT 0.896435 -137 ACTTATAATAAATATAGTTTTTATTTTTATTAATA 5 77 0 AATTTTTATT 0.874775 -112 agatgactttgatagttattagtaattaat 6 6 1 actttgtatt 0.879923 -152 acactttaccaatctaattgctgatctctagcagt 7 18 0 aatttgtgat 0.967986 -283 agaacattttaatctcgtagttgatgcccacctaa 7 117 1 aatttgtgat 0.967989 -184 tgcccacctaaatcgcgtttgtgatggtccagccc 7 141 1 aatgtttgat 0.750772 -160 gcgaggtcaaaatttcgtcgatgtgaatttattat 7 178 0 aatttgtgtg 0.869535 -123 atttcgtgacaatgtttttgcgaatttccattcga 7 222 1 aatttggaat 0.829052 -79 agggaaaggaaatttgttcgttattacactagatc 7 271 0 aatttgtatt 0.961891 -30 *** * * * **** Masking position 1 Map Score: 9.16454 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 178 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 GCGATATTAGCACCAAACAAAAACGACAATC 1 139 0 CACCAACAAA 0.964598 -162 AATAGGTAAGCACCAAGCAAAAATTAAGGAC 1 244 1 CACCAACAAA 0.964598 -57 AATTTAAATTAAGCACTCATACTAATATATT 2 62 1 AAGCACCATA 0.931489 -76 TTAAAGAGTTAAGCAATCTAAAGGGATTAAT 2 90 0 AAGCAACTAA 0.87374 -48 aattagttaacagcccacttaaggtggttgt 6 38 1 cagcccctta 0.959168 -120 cccacaaaatcagcccccaaacttataataa 6 79 0 cagccccaaa 0.988422 -79 tcaaggggtgaaccccacaaaatcagccccc 6 92 0 aacccccaaa 0.964208 -66 tatcacactttaccaatctaattgctgatct 7 26 0 taccaactaa 0.68858 -275 tgtgatggtccagcccccataataaattcac 7 160 1 cagccccata 0.978157 -141 ****** **** Masking position 2 Map Score: 8.44031 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 38 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 TTGCTCGAGGACTTATTGGTTGATAAAAGGTATT 1 93 1 ACTTTGTGAT 0.915018 -208 AAAAACGACAATCTTTTAGTTGATAAATACCTTT 1 118 0 ATTTTGTGAT 0.978699 -183 CGCAAAGGATGTTTTAGGCATTAACAATGTCT 4 67 0 ATTTTGCATT 0.832977 -22 AAGTTAAATGGCTTTGTTAATTTGTTTAGAT 5 8 1 ATGTTGTAAT 0.8932 -181 AATTCTCTCGATATTTTCGATATTTAAATCTATA 5 43 0 ATTTTGTATT 0.949436 -146 cactttaccaatctaattgctgatctctagcagt 7 18 0 attatgtgat 0.89199 -283 gaacattttaatctcgtagttgatgcccacctaa 7 118 1 attgtgtgat 0.924413 -183 tttcgtgacaatgtttttgcgaatttccattcga 7 223 1 attttggaat 0.904829 -78 gggaaaggaaatttgttcgttattacactagatc 7 271 0 attttgtatt 0.949436 -30 ** * ** * **** Masking position 7 Map Score: 2.82396 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 56 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 CTATGCTTACACCTGTAACCTATCAACGTC 1 37 0 ACCTGTAACC 0.989388 -264 CTGTGGAAACACCTGGAACCATCCCGAACC 1 169 1 ACCTGGAACC 0.990161 -132 ACCTGGAACCATCCCGAACCCAGCAGTTAA 1 179 1 ATCCCGAACC 0.9325 -122 AGAATTTATTACTTCTAACCTTGGCAATGA 5 126 1 ACTTCTAACC 0.965984 -63 aagaccattgatttgtaaccgcggttgaaa 7 59 0 atttgtaacc 0.948361 -242 ********** Masking position 7 Map Score: 2.04112 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 TATTAGCACCAAACAAAAACGACAATCTTT 1 136 0 AAACAAAAAC 0.939742 -165 TTAAATAAAAAAAGACCATAGGTTTT 1 285 0 AAAAAAAGAC 0.939742 -16 TTAATGGACTTAAAAAAGACATTGTTAATG 4 51 1 TAAAAAAGAC 0.922941 -38 CTAAACAAATTAACAAAGCCATTTAACTT 5 10 0 TAACAAAGCC 0.892514 -179 TTATTAATAAAAATAAAAACTATATTTATT 5 76 1 AAATAAAAAC 0.873764 -113 TAATTAATAAACACGTTGAATTAT 5 175 0 TAATAAACAC 0.891569 -14 aaataaaccaaaacaaccaccttaagtggg 6 51 0 aaacaaccac 0.881274 -107 ********** Masking position 5 Map Score: 1.40809 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 115 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 GTAACCTATCAACGTCATGGTCTATAACGGCTC 1 20 0 AATATGGTCT 0.986525 -281 GCACCAAGCAAAAATTAAGGACTATAGGTTTAA 1 253 1 AATAAGGACT 0.939501 -48 ATAGGTTTAAAAACCTATGGTCTTTTTTTATTT 1 276 1 AACATGGTCT 0.984563 -25 AAATTACTCTGATTTAATGGACTTAAAAAAGAC 4 38 1 GATATGGACT 0.958363 -51 ccgcggttacaaatcaatggtctttcagaaaac 7 65 1 aacatggtct 0.987149 -236 ** * ******* Masking position 7 Map Score: 0.376673 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 TGTTGAGCTGAGTAATACTAATTGCTCGAG 1 72 1 AGTAATACTA 0.781209 -229 CTTTTAGTTGATAAATACCTTTTATCAACC 1 110 0 ATAAATACCT 0.869909 -191 TATTCTCAGTATTACTACCTACATTTAGCT 1 218 0 ATTACTACCT 0.908354 -83 ATACTAATATATTAATCCCTTTAGATTGCT 2 80 1 ATTAATCCCT 0.955898 -58 TTGAAGTAAAATTAATCCTA 3 15 1 ATTAATCCTA 0.886474 -10 GAGTAATTTTATTAATATTTATCTAACTTA 4 17 0 ATTAATATTT 0.77578 -72 gaattaatacttgttgaattat 6 146 0 attaatactt 0.963865 -12 ********** Masking position 4 Map Score: 1.19951 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 77 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: 2.95118e-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: 2.95118e-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 11 ********** No masking Map Score: 2.95118e-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