AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i079_Phospholipid_Biosynthesis_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 psd 60 psd #2 Rv0439c 293 hypothetical protein Rv0439c Motif number 1 CGTGCCGCAGGTTGGGTGCACGGCACTAGG 1 21 0 GTTGGGTGCA 0.874146 -40 GCCGTCACCCGGTGACCCCCGTTTCATCCC 2 34 0 GGTGACCCCC 0.820758 -260 GGGGTCACCGGGTGACGGCAACCCCGCTAC 2 45 1 GGTGACGGCA 0.987561 -249 ACTTACGCTGGCCGGGCGCAGTGCCCGCGA 2 73 1 GCCGGGCGCA 0.875423 -221 TGAGCCGTCCGTCGCGGGCACTGCGCCCGG 2 84 0 GTCGCGGGCA 0.97462 -210 AGCGAGTGGCAGCGAGGACAACTTGAGCCG 2 107 0 AGCGAGGACA 0.943654 -187 CCGTCGTCGCAGCGAGTGGCAGCGAGGACA 2 117 0 AGCGAGTGGC 0.96499 -177 CACTCGCTGCGACGACGGGCCTGGCCTCAC 2 129 1 GACGACGGGC 0.930918 -165 AGGTCGGGACGGTGAGGCCAGGCCCGTCGT 2 140 0 GGTGAGGCCA 0.98336 -154 ACTCGCGACCGGTGAGTGCTAGGTCGGGAC 2 160 0 GGTGAGTGCT 0.977104 -134 ACTCACCGGTCGCGAGTGCCAACGTTATTC 2 173 1 CGCGAGTGCC 0.979406 -121 ACTCGGCATAGGCGAGTGCTAAGAATAACG 2 195 0 GGCGAGTGCT 0.989017 -99 ACTCGCCTATGCCGAGTGCAAGAAGCCCCG 2 208 1 GCCGAGTGCA 0.992937 -86 GGCATGACCCGGTGCGGGGCTTCTTGCACT 2 222 0 GGTGCGGGGC 0.940547 -72 GACACGGTCGAACGAGGGGCATGACCCGGT 2 239 0 AACGAGGGGC 0.902736 -55 GGATCGGAGGGCCGAGGACACGGTCGAACG 2 255 0 GCCGAGGACA 0.97215 -39 ********** Masking position 4 Map Score: 29.7953 Number of sites scoring better than the average of aligned sites = 19127 Number in coding regions = 17833 Number in noncoding regions = 1294 Number of orfs with sites within 600 bp upstream = 833 Fraction of orfs with sites within 600 bp upstream = 0.133794 Motif number 2 ACGGCACTAGGATCGGTCCGG 1 1 0 GTCGGTCCGG 0.990234 -60 TCTTACGGAGCTTCGTGCCGCAGGTTGGGTG 1 33 0 CTCGTGCCGC 0.991261 -28 CCCGTTTCATCCCCGATCCGGAGGAATCACT 2 16 0 CCCGATCCGG 0.991063 -278 GTTGCCGTCACCCGGTGACCCCCGTTTCATC 2 36 0 CCGGTGACCC 0.891801 -258 GCTGGCCGGGCGCAGTGCCCGCGACGGACGG 2 79 1 CCAGTGCCCG 0.986389 -215 GGGACGGTGAGGCCAGGCCCGTCGTCGCAGC 2 134 0 GCCAGGCCCG 0.992806 -160 GTGAGTGCTAGGTCGGGACGGTGAGGCCAGG 2 148 0 GTCGGGACGG 0.97947 -146 ACCTAGCACTCACCGGTCGCGAGTGCCAACG 2 166 1 CCCGGTCGCG 0.978652 -128 CCCCGCACCGGGTCATGCCCCTCGTTCGACC 2 233 1 GTCATGCCCC 0.945874 -61 CCCCTCGTTCGACCGTGTCCTCGGCCCTCCG 2 250 1 GCCGTGTCCT 0.883968 -44 GTCCTCGGCCCTCCGATCCGGGTGAGTATGT 2 266 1 CCCGATCCGG 0.991088 -28 * ********* Masking position 9 Map Score: 15.1138 Number of sites scoring better than the average of aligned sites = 26732 Number in coding regions = 24941 Number in noncoding regions = 1791 Number of orfs with sites within 600 bp upstream = 977 Fraction of orfs with sites within 600 bp upstream = 0.156923 Motif number 3 CAGGTTGGGTGCACGGCACTAGGATCGGTCCGG 1 11 0 GCAGGCACGG 0.994782 -50 CCAACCTGCGGCACGAAGCTCCGTAAGATGACC 1 36 1 GCAGAAGCCG 0.994146 -25 TCCCCGATCCGGAGGAATCACTTCGCA 2 5 0 GGAGAATCTT 0.694172 -289 TCCGGATCGGGGATGAAACGGGGGTCACCGGGT 2 25 1 GGAGAAACGG 0.979574 -269 CCCGGCCAGCGTAAGTAGCGGGGTTGCCGTCAC 2 56 0 GTAGTAGCGG 0.898424 -238 TCCGTCGCGGGCACTGCGCCCGGCCAGCGTAAG 2 74 0 GCATGCGCGG 0.980229 -220 TGCCCGCGACGGACGGCTCAAGTTGTCCTCGCT 2 94 1 GGAGGCTCGT 0.944629 -200 GGACGGTGAGGCCAGGCCCGTCGTCGCAGCGAG 2 131 0 GCCGGCCCCG 0.972025 -163 TATGCCGAGTGCAAGAAGCCCCGCACCGGGTCA 2 215 1 GCAGAAGCCG 0.994146 -79 CGAACGAGGGGCATGACCCGGTGCGGGGCTTCT 2 228 0 GCAGACCCTG 0.984319 -66 *** ***** ** Masking position 9 Map Score: 11.4294 Number of sites scoring better than the average of aligned sites = 4810 Number in coding regions = 4398 Number in noncoding regions = 412 Number of orfs with sites within 600 bp upstream = 325 Fraction of orfs with sites within 600 bp upstream = 0.0522004 Motif number 4 TGCGAAGTGATTCCTCCGGATCGGGGATG 2 10 1 ATTCCTCCGG 0.709842 -284 GATGAAACGGGGGTCACCGGGTGACGGCAA 2 36 1 GGGTCACCGG 0.965691 -258 GCACTGCGCCCGGCCAGCGTAAGTAGCGGG 2 67 0 CGGCCAGCGT 0.913601 -227 GGACAACTTGAGCCGTCCGTCGCGGGCACT 2 92 0 AGCCGTCCGT 0.961295 -202 GGTGAGGCCAGGCCCGTCGTCGCAGCGAGT 2 130 0 GGCCCGTCGT 0.95581 -164 GACGGGCCTGGCCTCACCGTCCCGACCTAG 2 142 1 GCCTCACCGT 0.947398 -152 CCGGTCGCGAGTGCCAACGTTATTCTTAGC 2 178 1 GTGCCAACGT 0.961482 -116 CATGCCCCTCGTTCGACCGTGTCCTCGGCC 2 246 1 GTTCGACCGT 0.95555 -48 CCGTGTCCTCGGCCCTCCGATCCGGGTGAG 2 262 1 GGCCCTCCGA 0.980749 -32 GGGCCGAACATACTCACCCGG 2 283 0 GGCCGAACAT 0.827729 -11 ********** Masking position 8 Map Score: 6.00668 Number of sites scoring better than the average of aligned sites = 15783 Number in coding regions = 14696 Number in noncoding regions = 1087 Number of orfs with sites within 600 bp upstream = 737 Fraction of orfs with sites within 600 bp upstream = 0.118375 Motif number 5 CACCGTCCCGACCTAGCACTCACCGGTCGC 2 156 1 ACCTAGCACT 0.992807 -138 CCAACGTTATTCTTAGCACTCGCCTATGCC 2 191 1 TCTTAGCACT 0.988918 -103 GGTGCGGGGCTTCTTGCACTCGGCATAGGC 2 212 0 TTCTTGCACT 0.980625 -82 ********** Masking position 8 Map Score: 0.766667 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 12 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 ********** No masking Map Score: -3.31523e-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: -3.31523e-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: -3.31523e-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