AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i069_Serine_Metabolism_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yloU 276 similar to alkaline-shock protein #2 yloW 138 similar to phosphoglycerate dehydrogenase #3 ylpA 25 similar to L-serine dehydratase Motif number 1 AAACGTTTTTTAGCTGTGGTAAATTATTTA 1 89 0 TAGCTGTGGT 0.969522 -188 ACATATACTATAGCGCTGCTGTTTCCGCAA 1 163 0 TAGCGCTGCT 0.990731 -114 ACCAGGCAATAATCGCTGGCCGTACCTCTA 1 192 0 AATCGCTGGC 0.960612 -85 TATAGTAGAATAGCTGTAACTCTATGCATT 1 241 1 TAGCTGTAAC 0.82304 -36 GGGCGCGTTACAGCGCTGCCGCACTTAAAA 2 44 0 CAGCGCTGCC 0.986965 -95 TCTAGAAGCAAAGCGCTAATAAGCTCTGGT 2 102 1 AAGCGCTAAT 0.949623 -37 AAGCGCTAATAAGCTCTGGTTCATAAGGAG 2 112 1 AAGCTCTGGT 0.986909 -27 ********** Masking position 2 Map Score: 5.66487 Number of sites scoring better than the average of aligned sites = 1069 Number in coding regions = 1018 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 TTGTTTCCCTCCTCACTTGCACAAA 1 6 1 TCCCTCCTCA 0.991693 -271 ACTAGTTCCTCCTTCGAATGCATAG 1 262 0 TTCCTCCTTC 0.993009 -15 GCTATTCCTCCTTATGAACCAGAG 2 125 0 TTCCTCCTTA 0.995887 -14 AACTGGCTCCTCCTGACCCTTTTCG 3 10 0 CTCCTCCTGA 0.991693 -16 ********** Masking position 5 Map Score: 4.50828 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 38 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TGTTAAAAAGTAGATGTTTTGTGCAAGTGA 1 23 0 TAGATGTTTT 0.953944 -254 CATATAATCTTAGATGCTTTCGATATGGAT 1 55 1 TAGATGCTTT 0.990833 -222 GCTTTCGATATGGATACTTTAAATAATTTA 1 70 1 TGGATACTTT 0.947511 -207 GCTATTCTACTATATGGTTTCCATTATGAA 1 225 0 TATATGGTTT 0.951273 -52 TAGCTGTAACTCTATGCATTCGAAGGAGGA 1 251 1 TCTATGCATT 0.908658 -26 TCTATTCTTATGTCTGCTTTTAAGTGCGGC 2 27 1 TGTCTGCTTT 0.964455 -112 ********** Masking position 5 Map Score: 3.41426 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 415 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 AGAAAATTCACTTGACATCTTGCGGAAACAG 1 144 1 CTTGACTCTT 0.91271 -133 GCAATAATCGCTGGCCGTACCTCTACATATA 1 186 0 CTGGCCTACC 0.975483 -91 CGATTATTGCCTGGTCTTTTCATAATGGAAA 1 207 1 CTGGTCTTTC 0.968008 -70 AAGGGCAATTTGCCCTTCTATTCTTATGT 2 9 1 TTTGCCTTCT 0.939523 -130 AACGCGCCCGCTTGCCATTTTATATCTGATC 2 65 1 CTTGCCTTTT 0.991812 -74 CTGGCTCCTCCTGACCCTTTTCG 3 3 0 CTGACCTTTT 0.967176 -23 ****** **** Masking position 8 Map Score: 1.31354 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 697 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 ATATACTATAGCGCTGCTGTTTCCGCAAGA 1 161 0 GCGCTGCTGT 0.991303 -116 GCGCGTTACAGCGCTGCCGCACTTAAAAGC 2 42 0 GCGCTGCCGC 0.962969 -97 CAGCGCTGTAACGCGCCCGCTTGCCATTTT 2 56 1 ACGCGCCCGC 0.732078 -83 ********** Masking position 4 Map Score: 0.569475 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 142 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 6 TAGATGTTTTGTGCAAGTGAGGAGGGAAAC 1 13 0 GTGCAAGTGA 0.970753 -264 GAAACAATAGTTGCAAACGTTTTTTAGCTG 1 103 0 TTGCAAACGT 0.866059 -174 TTCCGCAAGATGTCAAGTGAATTTTCTTGA 1 141 0 TGTCAAGTGA 0.933677 -136 TGTAGAGGTACGGCCAGCGATTATTGCCTG 1 190 1 CGGCCAGCGA 0.967734 -87 AAGAATAGAAGGGCAAATTGCCCTT 2 6 0 GGGCAAATTG 0.847175 -133 AGATATAAAATGGCAAGCGGGCGCGTTACA 2 62 0 TGGCAAGCGG 0.993171 -77 ********** Masking position 6 Map Score: 0.053648 Number of sites scoring better than the average of aligned sites = 1195 Number in coding regions = 1089 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 ********** No masking Map Score: 9.48026e-14 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: 9.48026e-14 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 9 ********** No masking Map Score: 9.48026e-14 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