AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i165_Nitrate_Reductase_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 narJ 25 nitrate reductase (protein J) #2 narG 195 nitrate reductase (alpha subunit) #3 ywiD 143 ywiD Motif number 1 CTTTTGATAAATGAGGTGTAACAAG 1 9 1 AAATGAGTGT 0.84187 -17 ATAGAGCCGGTTTTTTTTGATCT 2 3 1 AGAGCCGTTT 0.88376 -193 TCTTTGAATGAAAGGCAGCTAATGACCCAAG 2 31 1 AAAGGCGCTA 0.971713 -165 CTGCGTTCAGGCAGGACGCTTGGGTCATTAG 2 49 0 GCAGGAGCTT 0.961726 -147 AAAGGAGAAGGAAGGCTGCGTTCAGGCAGGA 2 64 0 GAAGGCGCGT 0.990202 -132 ATTTTGTGAAAAAAGCAGAGTGTGTGACATA 2 103 1 AAAAGCGAGT 0.917621 -93 CACTATAAACAGAGACAGCGTGTTTCCTTGT 2 138 0 AGAGACGCGT 0.939324 -58 ATGAAAGAAAAAAGGAGGATTTCG 3 4 0 AAAGGAGATT 0.960962 -140 CATTCATCATACAGGCTGTGAAATACATCAC 3 65 1 ACAGGCGTGA 0.981454 -79 TCACTGCTGTACAGGCTCAGTCGAGCTACAC 3 92 1 ACAGGCCAGT 0.948923 -52 TATCCTTAGCACAGGAGGTTTTCCT 3 129 1 ACAGGAGTTT 0.975017 -15 ****** **** Masking position 3 Map Score: 11.3115 Number of sites scoring better than the average of aligned sites = 2814 Number in coding regions = 2483 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 2 CTTGTTACACCTCATTTATCA 1 15 0 TTGTTACACC 0.754251 -11 TTTCACAAAATGTTCACACAAAGGAGAAGG 2 84 0 TGTTCACACA 0.975795 -112 CACTCTGCTTTTTTCACAAAATGTTCACAC 2 95 0 TTTTCACAAA 0.93831 -101 CTTGTGAACTATGTCACACACTCTGCTTTT 2 113 0 ATGTCACACA 0.980167 -83 TGTGTGACATAGTTCACAAGGAAACACGCT 2 123 1 AGTTCACAAG 0.9439 -73 GGTGATGCTAAGTTCACTATAAACAGAGAC 2 153 0 AGTTCACTAT 0.85622 -43 GAGAGTTCACTCCTTCCGAGTCA 2 183 0 AGTTCACTCC 0.979946 -13 TGTATGATGAATGTCACTTATCAGGAGGGT 3 48 0 ATGTCACTTA 0.83244 -96 GCAGTGATGTATTTCACAGCCTGTATGATG 3 69 0 ATTTCACAGC 0.953597 -75 ********** Masking position 6 Map Score: 7.18254 Number of sites scoring better than the average of aligned sites = 764 Number in coding regions = 601 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 CCTGAACGCAGCCTTCCTTCTCCTTTGTGT 2 69 1 GCCTTCCTTC 0.940959 -127 CAGAGTGTGTGACATAGTTCACAAGGAAAC 2 118 1 GACATAGTTC 0.940185 -78 CGAAATCCTCCTTTTTTCTTT 3 2 1 GAAATCCTCC 0.989025 -142 CCTGATAAGTGACATTCATCATACAGGCTG 3 53 1 GACATTCATC 0.959583 -91 TACAGGCTGTGAAATACATCACTGCTGTAC 3 74 1 GAAATACATC 0.954518 -70 AGGAAAACCTCCTGTGCTAAGG 3 132 0 GAAAACCTCC 0.958124 -12 ********** Masking position 1 Map Score: 3.20381 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 570 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 ********** No masking Map Score: -7.57276e-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 5 ********** No masking Map Score: -7.57276e-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 6 ********** No masking Map Score: -7.57276e-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