AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i257_hsp60_hsp10_mgen_reg_300.orf -o257_mgen_300.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMG04338 167 Mycoplasma #2 RMG05439 300 Mycoplasma Motif number 1 TTTGTATTTAAAAATTAACAATATCTCA 1 8 1 TTAAAATTAA 0.884784 -160 ATCTCACTAAATATTAATTAATGTTTAGCGC 1 33 1 ATATAATTAA 0.974797 -135 AACTAATTTAAAAGAAAGTAAAAGTTATCTT 1 81 0 AAAAAAGTAA 0.870319 -87 TAATAATTAAAAACTAATTTAAAAGAAAGTA 1 92 0 AAATAATTTA 0.906866 -76 TAAAAATATTTTAATAATTAAAAACTAATTT 1 103 0 TTATAATTAA 0.733607 -65 AATTAAAACCAAAAAAATTAATCCCGTTAGA 2 35 0 AAAAAATTAA 0.975034 -266 TGACTCAGGTAAACTAACTAAATTAAAACCA 2 55 0 AAATAACTAA 0.93529 -246 ATCAAAAAAGTTAAAAATGAAAATAGAACTA 2 90 0 TTAAAATGAA 0.859976 -211 GCTAATGAAAAAACTAATGAAAGCAAATGCA 2 124 0 AAATAATGAA 0.984125 -177 TAAAAAGAAGAAGCTAATGAAAAAACTAATG 2 136 0 AAGTAATGAA 0.907241 -165 AAGCAGAATAAAAATAATTAAATTTATCAGT 2 182 1 AAATAATTAA 0.987176 -119 TTTAGCTTCAAAAATAATTGAGTTCATCTTT 2 215 0 AAATAATTGA 0.935397 -86 TCAAAACCTTTAATTAATGAAGTTAAGAAGC 2 263 0 TAATAATGAA 0.966306 -38 *** ******* Masking position 6 Map Score: 20.9862 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 353 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 TTGTTAATTTTTAAATACAAA 1 2 0 TTAAATACAA 0.384488 -166 CTAATATCAGATAAATTTAAGATAACTTTT 1 63 1 ATAAATTTAA 0.796339 -105 ACTAATTTAAAAGAAAGTAAAAGTTATCTT 1 81 0 AAGAAAGTAA 0.774911 -87 TTTTAATAATTAAAAACTAATTTAAAAGAA 1 96 0 TAAAAACTAA 0.68683 -72 TATTTTTATTATGAACATAACGCCAATTCA 1 126 1 ATGAACATAA 0.819908 -42 AAGTGAAACCAAGACGTTGTCA 1 156 0 GTGAAACCAA 0.829226 -12 AGTAGTTATCAAGCCAATGCAAATTCT 2 8 1 ATCAAGCCAA 0.802468 -293 ACTAACTAAATTAAAACCAAAAAAATTAAT 2 44 0 TTAAAACCAA 0.855885 -257 GCAACCATCAAAAAAGTTAAAAATGAAAAT 2 97 0 AAAAAGTTAA 0.774435 -204 GAAAAAACTAATGAAAGCAAATGCAACCAT 2 119 0 ATGAAAGCAA 0.903573 -182 AATTAAAAAGAAGAAGCTAATGAAAAAACT 2 140 0 AAGAAGCTAA 0.920112 -161 TTAGTTTTAGATGCAATTAAAAAGAAGAAG 2 154 0 ATGCAATTAA 0.693493 -147 TTAATTGCATCTAAAACTAAGCAGAATAAA 2 164 1 CTAAAACTAA 0.766368 -137 ACTAAGCAGAATAAAAATAATTAAATTTAT 2 179 1 ATAAAAATAA 0.854397 -122 CTTTTCACTGATAAATTTAATTATTTTTAT 2 189 0 ATAAATTTAA 0.796339 -112 CAGTGAAAAGATGAACTCAATTATTTTTGA 2 209 1 ATGAACTCAA 0.87628 -92 TCAATTATTTTTGAAGCTAAAGCCTAAGTT 2 225 1 TTGAAGCTAA 0.93014 -76 CCTTTAATTAATGAAGTTAAGAAGCACTTG 2 258 0 ATGAAGTTAA 0.953287 -43 ********** Masking position 5 Map Score: 15.6477 Number of sites scoring better than the average of aligned sites = 990 Number in coding regions = 904 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 AGACGTTGTCATGAATTGGCGTTATGTTCA 1 137 0 ATGAATTGGC 0.969511 -31 CCGTTAGAATTTGCATTGGCTTGATAACTA 2 13 0 TTGCATTGGC 0.996877 -288 TTTTTGATGGTTGCATTTGCTTTCATTAGT 2 113 1 TTGCATTTGC 0.991529 -188 TCATTAGTTTTTTCATTAGCTTCTTCTTTT 2 135 1 TTTCATTAGC 0.967165 -166 ********** Masking position 5 Map Score: 3.64558 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 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 4 TTTAGTGAGATATTGTTAATTTTTAAATAC 1 14 0 TATTGTTAAT 0.87997 -154 AAGTAAAAGTTATCTTAAATTTATCTGATA 1 67 0 TATCTTAAAT 0.79713 -101 ACTTTTACTTTCTTTTAAATTAGTTTTTAA 1 87 1 TCTTTTAAAT 0.942805 -81 ATTATTAAAATATTTTTATTATGAACATAA 1 116 1 TATTTTTATT 0.969114 -52 ATAGTAGTTCTATTTTCATTTTTAACTTTT 2 86 1 TATTTTCATT 0.974287 -215 CTTTCATTAGTTTTTTCATTAGCTTCTTCT 2 132 1 TTTTTTCATT 0.903363 -169 ATTAGCTTCTTCTTTTTAATTGCATCTAAA 2 149 1 TCTTTTTAAT 0.96851 -152 TAAATTTAATTATTTTTATTCTGCTTAGTT 2 178 0 TATTTTTATT 0.969114 -123 ATTGAGTTCATCTTTTCACTGATAAATTTA 2 200 0 TCTTTTCACT 0.943602 -101 ********** Masking position 6 Map Score: 11.3551 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 233 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 ********** No masking Map Score: 5.06917e-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 6 ********** No masking Map Score: 5.06917e-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: 5.06917e-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